https://megcore.nih.gov/api.php?action=feedcontributions&user=Jstout&feedformat=atomMEG Core - User contributions [en]2024-03-28T19:16:57ZUser contributionsMediaWiki 1.41.0https://megcore.nih.gov/index.php?title=Club_MEG&diff=5638Club MEG2024-03-24T16:19:01Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''04/19/2024 at 1:00pm''' 2X Journal Article<br />
** Shruti<br />
** Ryan<br />
*** [https://www.biorxiv.org/content/10.1101/2023.06.23.546249v2.full.pdf An adversarial collaboration to critically evaluate theories of consciousness ] <br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article<br />
** Lucrezia <br />
** Anna<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
* '''06/**/2024''' Check with Jess and Sebastian<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5637Club MEG2024-03-19T19:03:20Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''04/19/2024 at 1:00pm''' 2X Journal Article<br />
** Shruti<br />
** Ryan<br />
*** [https://www.biorxiv.org/content/10.1101/2023.06.23.546249v2.full.pdf An adversarial collaboration to critically evaluate theories of consciousness ] <br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article<br />
** Lucrezia <br />
** Anna<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5636Club MEG2024-03-19T18:48:32Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''04/19/2024 at 1:00pm''' 2X Journal Article<br />
** Shruti<br />
** Ryan<br />
*** [https://www.biorxiv.org/content/10.1101/2023.06.23.546249v2.full.pdf An adversarial collaboration to critically evaluate theories of consciousness ] <br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5635Club MEG2024-03-15T13:30:04Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''04/19/2024 at 1:00pm''' 2X Journal Article --- Shruti and Ryan<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5633Club MEG2024-03-08T18:35:00Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''04/19/2024 at 1:00pm''' 2X Journal Article --- Shruti and Ryan<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5622Club MEG2024-03-05T20:36:34Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal<br />
*** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui<br />
*** [https://www.pnas.org/doi/full/10.1073/pnas.1508523113 Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns]<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5621Club MEG2024-03-05T19:58:49Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez Andonegui [ ]<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5620Club MEG2024-03-05T19:48:12Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article<br />
** Shivam Bansal <br />
*** [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902297/pdf/42003_2024_Article_5927.pdf Linking structural and functional changes during aging using multilayer brain network analysis ]<br />
** Amaia Benitez<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5602Club MEG2024-02-27T20:47:33Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
<br />
Note to self: Don't schedule during these times: </br><br />
06/(23 - 27)/2024 OHBM </br><br />
08/(26 – 29)/2024 BIOMAG </br><br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5601Club MEG2024-02-27T19:08:22Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/**/2024 at 1:00pm''' 2X Journal Article --- Lucrezia and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5600Club MEG2024-02-27T18:08:22Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''04/**/2024 at 1:00pm''' 2X Journal Article --- Shruti and --<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5598Club MEG2024-02-26T14:07:50Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''02/23/2024''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''02/16/2024''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5589Club MEG2024-02-16T14:29:26Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
*** [https://www.sciencedirect.com/science/article/pii/S105381192200492X The natural frequencies of the resting human brain ] <br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5588Club MEG2024-02-15T14:40:09Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article<br />
** Fred Carver<br />
*** [https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D MEG-based neurofeedback for hand rehabilitation ]<br />
** Jeff Stout<br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5587Club MEG2024-02-15T14:38:39Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article<br />
** Fred Carver - MEG-based neurofeedback for hand rehabilitation<br />
*** https://www.biomedcentral.com/epdf/10.1186/s12984-015-0076-7?sharing_token=mkccASrrnNz9b8w0BMAJ82_BpE1tBhCbnbw3BuzI2RNVoDKPinmyo4Rqp7Gjl8B4zqtKDO-MMrgZh-FgW06gwuL_Dl39uXBVRbbC4vqoHXQJBKV6_KXny6x6KAlhDvqL4tZzdevxq1WLF85j0Mafb7m5Aoq0vs43lwARUHXqlYA%3D<br />
** Jeff Stout<br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5584Club MEG2024-02-14T17:00:44Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee - Dysregulated connectivity among insula, postcentral gyrus, and precuneus and its association with suicide risk<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Biowulf_standard_processing&diff=5580Biowulf standard processing2024-02-13T21:40:22Z<p>Jstout: </p>
<hr />
<div>= Quick tutorial to generate most of the needed inputs for data analysis =<br />
<br />
== General Setup ==<br />
=== Mounting local computer to biowulf ===<br />
https://hpc.nih.gov/docs/hpcdrive.html<br />
== Configuring your bash shell environment ==<br />
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.<br />
=== Edit .bashrc file in your home drive ===<br />
umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team<br />
<br />
#Add modules bin path to access the MEG modules<br />
PATH=/data/MEGmodules/bin:$PATH<br />
<br />
## Set up some aliases, so you don't have to type these out<br />
alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'<br />
alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'<br />
alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'<br />
<br />
=== Edit .bash_profile in your home drive ===<br />
#Set your default group (normally your default is your userID - which isn't helpful for your group<br />
#Type `groups` to see which groups you are part of<br />
newgrp <<YOUR GROUP ID>><br />
<br />
=== To Access Additional MEG modules ===<br />
#Add the following line to your ${HOME}/.bashrc<br />
module use --append /data/MEGmodules/modulefiles<br />
<br />
== General Processing Pipeline == <br />
=== First write out the appropriate events in the markerfile ===<br />
TBD - fill in items here<br />
<br />
=== Convert Data to BIDS === <br />
module load mne<br />
make_meg_bids.py -h #Then fill in the required items<br />
<br />
== Processing the MRI related components == <br />
#Generate Bounary Element Model / Transform / Forward model for source localization. Check the help, there is a volume vs surface flag<br />
#This will write out the swarmfile (which can be editted) -- and prints out the command to launch the swarm job<br />
megcore_prep_mri_bids.py -gen_swarmfile -bids_root <<BIDS_ROOT>> -swarm_fname <<SWARM_FNAME>> -subject <<SUBJECT>> -run <<RUN>> -session <<SESSION>> -task <<TASK>><br />
<br />
<br />
<br />
<br />
<br />
<br />
== Parsing Logfiles ==<br />
Presentation Files:<br />
https://github.com/gjcooper/prespy</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5579Club MEG2024-02-13T20:52:05Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee<br />
* '''03/08/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5578Club MEG2024-02-13T20:50:28Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024 at 1:00pm''' Yoojin Lee<br />
* '''03/15/2024 at 1:00pm''' 2X Journal Article --- Shivam and Amaia<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Biowulf_standard_processing&diff=5577Biowulf standard processing2024-02-12T16:53:06Z<p>Jstout: </p>
<hr />
<div># Quick tutorial to generate most of the needed inputs for data analysis<br />
<br />
# Mounting local computer to biowulf<br />
https://hpc.nih.gov/docs/hpcdrive.html<br />
<br />
<br />
# Parsing Logfiles<br />
https://github.com/gjcooper/prespy</div>Jstouthttps://megcore.nih.gov/index.php?title=Biowulf_standard_processing&diff=5576Biowulf standard processing2024-02-09T18:04:10Z<p>Jstout: Created page with "# Quick tutorial to generate most of the needed inputs for data analysis # Parsing Logfiles https://github.com/gjcooper/prespy"</p>
<hr />
<div># Quick tutorial to generate most of the needed inputs for data analysis<br />
<br />
<br />
# Parsing Logfiles<br />
https://github.com/gjcooper/prespy</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5575Club MEG2024-02-06T19:06:18Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024''' Yoojin Lee<br />
* '''05/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5574Club MEG2024-02-06T18:44:53Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''02/16/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5573Club MEG2024-01-26T21:07:38Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''02/09/2024 at 1:00pm''' 2X Journal Article -- Fred and Jeff<br />
* '''02/23/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5572Club MEG2024-01-26T20:52:41Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''02/09/2024?? at 1:00pm''' --- Journal Article<br />
* '''02/23/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_analysis_on_Biowulf&diff=5571MEG analysis on Biowulf2024-01-26T16:03:22Z<p>Jstout: /* Edit .bashrc file in your home drive */</p>
<hr />
<div>== Biowulf brief intro ==<br />
Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br><br />
#For processing of data - reserve an sinteractive session<br />
sinteractive --mem=6G --cpus-per-task=4<br />
<br />
#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option<br />
Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br><br />
#Use scp for transfer or rsync -av (slower but some benefits)<br />
scp -r ./my_local_results ${USERNAME}@helix.nih.gov:/data/mydatafolder/.... <br />
<br />
#Getting results from biowulf cluster<br />
scp -r ${USERNAME}@helix.nih.gov:/data/mydatafolder/... ${PATH_OFSTUFF}/my_local_stuff<br />
<br />
Analysis of data should not be performed on the biowulf head node, but run through an sinteractive node or swarm process. <br><br />
To start with, there are a limited number of commands loaded on the system. To access more programs use module load. To search, use module spider.<br />
e.g. module load afni<br />
<br />
== Configuring your bash shell environment ==<br />
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.<br />
=== Edit .bashrc file in your home drive ===<br />
umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team<br />
<br />
#Add modules bin path to access the MEG modules<br />
PATH=/data/MEGmodules/bin:$PATH<br />
<br />
## Set up some aliases, so you don't have to type these out<br />
alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'<br />
alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'<br />
alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'<br />
<br />
=== Edit .bash_profile in your home drive ===<br />
#Set your default group (normally your default is your userID - which isn't helpful for your group<br />
#Type `groups` to see which groups you are part of<br />
newgrp <<YOUR GROUP ID>> <br />
<br />
<br />
<br />
== SAM MEG Data Analysis ==<br />
module load afni <br />
module load ctf<br />
module load samsrcv3/20180713-c5e1042<br />
<br />
== MNE python data analysis ==<br />
===To Access Additional MEG modules===<br />
#Add the following line to your ${HOME}/.bashrc<br />
module use --append /data/MEGmodules/modulefiles<br />
<br />
===Load MNE modules===<br />
#The module will not load on the biowulf head-node because freesurfer loads<br />
#Create an sinteractive or spersist node - adjust memory and cpus core number accordingly<br />
sinteractive --mem=6G --cpus-per-task=4 <br />
module load mne/0.24.1 # OR module load mne <<-- defaults to most current version<br />
<br />
ipython<br />
import mne<br />
<br />
===Load Commandline MNE scripts for Processing Data===<br />
!Currently in Beta Testing!<br />
[stoutjd@cn1023 modules]$ module list <br />
No modules loaded<br />
[stoutjd@cn1023 modules]$ module load mne_scripts<br />
[+] Loading freesurfer 7.1.1 on cn1023 <br />
[+] Loading mne 0.24.1 ... <br />
[+] Loading mne_scripts 0.1_dev ... <br />
Available:<br />
spatiotemporal_clustering_stats.py<br />
[stoutjd@cn1023 modules]$ spatiotemporal_clustering_stats.py -h <br />
usage: spatiotemporal_clustering_stats.py [-h] [-topdir TOPDIR] [-search SEARCH]<br />
[-outfname OUTFNAME]<br />
[-subjects_dir SUBJECTS_DIR]<br />
<br />
options:<br />
-h, --help show this help message and exit<br />
-topdir TOPDIR The directory w/ stc files<br />
-search SEARCH The search term to find the specific stc files for clustering<br />
-outfname OUTFNAME Output filename for the cluster nifti file<br />
-subjects_dir SUBJECTS_DIR<br />
Freesurfer subjects dir. Will download freesurfer average if not<br />
already present. Defaults to os.environ['SUBJECTS_DIR'] if not<br />
provided<br />
<br />
===MNE bids creation and MNE bids pipeline processing on biowulf===<br />
====Start interactive session with scratch to render visualization offscreen====<br />
sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50<br />
<br />
====Create BIDS data from data off the scanner====<br />
module load mne_scripts<br />
make_meg_bids.py -meg_input_dir MEGFOLDER -mri_brik AFNI_COREGED+orig.BRIK<br />
<br />
====Process data using MNE Bids Pipeline====<br />
module purge <br />
module load mne_bids_pipeline<br />
mne-bids-pipeline-run.py --config=CONFIG.py ##Optional --steps=preprocessing,source --subject=SUBJECTID(without sub-)<br />
<br />
==Best Practices for Group Data Preprocessing==<br />
===Process your project data===<br />
====Make your python script commandline callable====<br />
#It is typical to run 1 subject per commandline call and to parrallelize over subjects in the swarm file<br />
-Use [https://docs.python.org/3/library/argparse.html argpase] to manually build a full commandline call with keyword inputs and function description <br />
-Use [https://google.github.io/python-fire/guide/ fire] or [https://click.palletsprojects.com/en/8.0.x/ click] to automatically create a commandline call based on function inputs<br />
-Use sys.argv[] to create a simple commandline input (sys.argv[0] is the filename - argv[1] is the first argument - argv[2] is second...)<br />
<br />
Helpful Hints: <br />
-Use the meg dataset as an input, inside the python module - use the meg dataset to extract the subject ID :<br />
filename = os.path.basename(meg_dataset) <br />
subjid = filename.split('_')[0] OR if you have a custom ID subjid = filename[0:#characters]<br />
-Build output filenames using f-strings: <br />
outfile_base = f'{subjid}_{taskname}.nii'<br />
outfilename = os.path.join(outdir, outfile_base)<br />
<br />
====Build, test, and submit your swarm file====<br />
for i in ${GROUP_FOLDER}/*.ds; do echo my_process.py -in1 input1 -in2 -input2 -dataset $i >> swarm_file_preprocess.sh ; done<br />
<br />
#Make sure the process runs on at least one subject/dataset<br />
#This will run the last line of the swarmfile<br />
$(tail -1 ./swarm_file_preprocess.sh) <br />
<br />
#Verify the results on the single subject / possibly look at how much RAM / CPU was used before submitting the full batch to swarm<br />
swarm -f ./swarm_file_preprocess.sh -g ${GigsOfRAM} -t ${CPUcores} # -b ${How many subjects to run in row on 1 computer} - can be useful if you have a fast process<br />
<br />
== ADVANCED: Making your own python module ==<br />
=== Build the python conda environment ===<br />
It is recommended to create an install script so that this can be sent to a slurm job<br />
# Load conda - if set up according to the HPC page, this should work<br />
source /data/${USER}/conda/etc/profile.d/conda.sh; conda activate base<br />
<br />
# echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1 -y > installFile.sh<br />
# Make sure to include the -y or the job will hang waiting for user response<br />
# Also make sure you have an active conda prompt when submitting the swarm, or else it will fail<br />
echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y > python_install.sh<br />
swarm -f ./python_install.sh -g 4 -t 4<br />
=== Make a module file ===<br />
To display most of the contents of a module file run <br />
module display python #For the python module<br />
Output:<br />
----------------------------------------------------------------------------------<br />
/usr/local/lmod/modulefiles/python/3.8.lua:<br />
----------------------------------------------------------------------------------<br />
family("python")<br />
prepend_path("PATH","/usr/local/Anaconda/envs/py3.8/bin")<br />
pushenv("OMP_NUM_THREADS","1")<br />
Copy Template to your module folder<br />
#MyModule is the family name of the code / ${Version}.lua<br />
cp /usr/local/lmod/modulefiles/python/3.8.lua ${myModuleFilesDir}/${MyModule}/0.1.lua<br />
<br />
=== Add module files to the search path ===<br />
module use --append ${PathToUserModuleFiles}<br />
<br />
=== Final Step Load Your Module ===<br />
# !! The module load process does not give good feedback that it doesn't load - make sure the path in lua file is correct !!<br />
module load ${MyModuleName}<br />
<br />
#Example<br />
[$USERd@$NODE python_modules]$ module load mne<br />
<br />
[$USERd@$NODE python_modules]$ ipython<br />
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11) <br />
Type 'copyright', 'credits' or 'license' for more information<br />
IPython 8.1.1 -- An enhanced Interactive Python. Type '?' for help.<br />
<br />
In [1]: import mne<br />
<br />
In [2]: mne.__path__<br />
Out[2]: ['/data/ML_MEG/python_modules/mne0.24.1/lib/python3.9/site-packages/mne']</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_analysis_on_Biowulf&diff=5570MEG analysis on Biowulf2024-01-26T16:03:04Z<p>Jstout: /* Edit .bashrc file in your home drive */</p>
<hr />
<div>== Biowulf brief intro ==<br />
Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br><br />
#For processing of data - reserve an sinteractive session<br />
sinteractive --mem=6G --cpus-per-task=4<br />
<br />
#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option<br />
Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br><br />
#Use scp for transfer or rsync -av (slower but some benefits)<br />
scp -r ./my_local_results ${USERNAME}@helix.nih.gov:/data/mydatafolder/.... <br />
<br />
#Getting results from biowulf cluster<br />
scp -r ${USERNAME}@helix.nih.gov:/data/mydatafolder/... ${PATH_OFSTUFF}/my_local_stuff<br />
<br />
Analysis of data should not be performed on the biowulf head node, but run through an sinteractive node or swarm process. <br><br />
To start with, there are a limited number of commands loaded on the system. To access more programs use module load. To search, use module spider.<br />
e.g. module load afni<br />
<br />
== Configuring your bash shell environment ==<br />
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.<br />
=== Edit .bashrc file in your home drive ===<br />
umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team<br />
<br />
#Add modules bin path to access the MEG modules<br />
PATH=/data/MEGmodules/bin:$PATH<br />
<br />
## Set up some aliases, so you don't have to type these out<br />
alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'<br />
alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'<br />
alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'<br />
<br />
=== Edit .bash_profile in your home drive ===<br />
#Set your default group (normally your default is your userID - which isn't helpful for your group<br />
#Type `groups` to see which groups you are part of<br />
newgrp <<YOUR GROUP ID>> <br />
<br />
<br />
<br />
== SAM MEG Data Analysis ==<br />
module load afni <br />
module load ctf<br />
module load samsrcv3/20180713-c5e1042<br />
<br />
== MNE python data analysis ==<br />
===To Access Additional MEG modules===<br />
#Add the following line to your ${HOME}/.bashrc<br />
module use --append /data/MEGmodules/modulefiles<br />
<br />
===Load MNE modules===<br />
#The module will not load on the biowulf head-node because freesurfer loads<br />
#Create an sinteractive or spersist node - adjust memory and cpus core number accordingly<br />
sinteractive --mem=6G --cpus-per-task=4 <br />
module load mne/0.24.1 # OR module load mne <<-- defaults to most current version<br />
<br />
ipython<br />
import mne<br />
<br />
===Load Commandline MNE scripts for Processing Data===<br />
!Currently in Beta Testing!<br />
[stoutjd@cn1023 modules]$ module list <br />
No modules loaded<br />
[stoutjd@cn1023 modules]$ module load mne_scripts<br />
[+] Loading freesurfer 7.1.1 on cn1023 <br />
[+] Loading mne 0.24.1 ... <br />
[+] Loading mne_scripts 0.1_dev ... <br />
Available:<br />
spatiotemporal_clustering_stats.py<br />
[stoutjd@cn1023 modules]$ spatiotemporal_clustering_stats.py -h <br />
usage: spatiotemporal_clustering_stats.py [-h] [-topdir TOPDIR] [-search SEARCH]<br />
[-outfname OUTFNAME]<br />
[-subjects_dir SUBJECTS_DIR]<br />
<br />
options:<br />
-h, --help show this help message and exit<br />
-topdir TOPDIR The directory w/ stc files<br />
-search SEARCH The search term to find the specific stc files for clustering<br />
-outfname OUTFNAME Output filename for the cluster nifti file<br />
-subjects_dir SUBJECTS_DIR<br />
Freesurfer subjects dir. Will download freesurfer average if not<br />
already present. Defaults to os.environ['SUBJECTS_DIR'] if not<br />
provided<br />
<br />
===MNE bids creation and MNE bids pipeline processing on biowulf===<br />
====Start interactive session with scratch to render visualization offscreen====<br />
sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50<br />
<br />
====Create BIDS data from data off the scanner====<br />
module load mne_scripts<br />
make_meg_bids.py -meg_input_dir MEGFOLDER -mri_brik AFNI_COREGED+orig.BRIK<br />
<br />
====Process data using MNE Bids Pipeline====<br />
module purge <br />
module load mne_bids_pipeline<br />
mne-bids-pipeline-run.py --config=CONFIG.py ##Optional --steps=preprocessing,source --subject=SUBJECTID(without sub-)<br />
<br />
==Best Practices for Group Data Preprocessing==<br />
===Process your project data===<br />
====Make your python script commandline callable====<br />
#It is typical to run 1 subject per commandline call and to parrallelize over subjects in the swarm file<br />
-Use [https://docs.python.org/3/library/argparse.html argpase] to manually build a full commandline call with keyword inputs and function description <br />
-Use [https://google.github.io/python-fire/guide/ fire] or [https://click.palletsprojects.com/en/8.0.x/ click] to automatically create a commandline call based on function inputs<br />
-Use sys.argv[] to create a simple commandline input (sys.argv[0] is the filename - argv[1] is the first argument - argv[2] is second...)<br />
<br />
Helpful Hints: <br />
-Use the meg dataset as an input, inside the python module - use the meg dataset to extract the subject ID :<br />
filename = os.path.basename(meg_dataset) <br />
subjid = filename.split('_')[0] OR if you have a custom ID subjid = filename[0:#characters]<br />
-Build output filenames using f-strings: <br />
outfile_base = f'{subjid}_{taskname}.nii'<br />
outfilename = os.path.join(outdir, outfile_base)<br />
<br />
====Build, test, and submit your swarm file====<br />
for i in ${GROUP_FOLDER}/*.ds; do echo my_process.py -in1 input1 -in2 -input2 -dataset $i >> swarm_file_preprocess.sh ; done<br />
<br />
#Make sure the process runs on at least one subject/dataset<br />
#This will run the last line of the swarmfile<br />
$(tail -1 ./swarm_file_preprocess.sh) <br />
<br />
#Verify the results on the single subject / possibly look at how much RAM / CPU was used before submitting the full batch to swarm<br />
swarm -f ./swarm_file_preprocess.sh -g ${GigsOfRAM} -t ${CPUcores} # -b ${How many subjects to run in row on 1 computer} - can be useful if you have a fast process<br />
<br />
== ADVANCED: Making your own python module ==<br />
=== Build the python conda environment ===<br />
It is recommended to create an install script so that this can be sent to a slurm job<br />
# Load conda - if set up according to the HPC page, this should work<br />
source /data/${USER}/conda/etc/profile.d/conda.sh; conda activate base<br />
<br />
# echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1 -y > installFile.sh<br />
# Make sure to include the -y or the job will hang waiting for user response<br />
# Also make sure you have an active conda prompt when submitting the swarm, or else it will fail<br />
echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y > python_install.sh<br />
swarm -f ./python_install.sh -g 4 -t 4<br />
=== Make a module file ===<br />
To display most of the contents of a module file run <br />
module display python #For the python module<br />
Output:<br />
----------------------------------------------------------------------------------<br />
/usr/local/lmod/modulefiles/python/3.8.lua:<br />
----------------------------------------------------------------------------------<br />
family("python")<br />
prepend_path("PATH","/usr/local/Anaconda/envs/py3.8/bin")<br />
pushenv("OMP_NUM_THREADS","1")<br />
Copy Template to your module folder<br />
#MyModule is the family name of the code / ${Version}.lua<br />
cp /usr/local/lmod/modulefiles/python/3.8.lua ${myModuleFilesDir}/${MyModule}/0.1.lua<br />
<br />
=== Add module files to the search path ===<br />
module use --append ${PathToUserModuleFiles}<br />
<br />
=== Final Step Load Your Module ===<br />
# !! The module load process does not give good feedback that it doesn't load - make sure the path in lua file is correct !!<br />
module load ${MyModuleName}<br />
<br />
#Example<br />
[$USERd@$NODE python_modules]$ module load mne<br />
<br />
[$USERd@$NODE python_modules]$ ipython<br />
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11) <br />
Type 'copyright', 'credits' or 'license' for more information<br />
IPython 8.1.1 -- An enhanced Interactive Python. Type '?' for help.<br />
<br />
In [1]: import mne<br />
<br />
In [2]: mne.__path__<br />
Out[2]: ['/data/ML_MEG/python_modules/mne0.24.1/lib/python3.9/site-packages/mne']</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_analysis_on_Biowulf&diff=5569MEG analysis on Biowulf2024-01-26T15:48:16Z<p>Jstout: /* Edit .bashrc file in your home drive */</p>
<hr />
<div>== Biowulf brief intro ==<br />
Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br><br />
#For processing of data - reserve an sinteractive session<br />
sinteractive --mem=6G --cpus-per-task=4<br />
<br />
#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option<br />
Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br><br />
#Use scp for transfer or rsync -av (slower but some benefits)<br />
scp -r ./my_local_results ${USERNAME}@helix.nih.gov:/data/mydatafolder/.... <br />
<br />
#Getting results from biowulf cluster<br />
scp -r ${USERNAME}@helix.nih.gov:/data/mydatafolder/... ${PATH_OFSTUFF}/my_local_stuff<br />
<br />
Analysis of data should not be performed on the biowulf head node, but run through an sinteractive node or swarm process. <br><br />
To start with, there are a limited number of commands loaded on the system. To access more programs use module load. To search, use module spider.<br />
e.g. module load afni<br />
<br />
== Configuring your bash shell environment ==<br />
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.<br />
=== Edit .bashrc file in your home drive ===<br />
umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team<br />
<br />
## Set up some aliases, so you don't have to type these out<br />
alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'<br />
alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'<br />
alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'<br />
<br />
=== Edit .bash_profile in your home drive ===<br />
#Set your default group (normally your default is your userID - which isn't helpful for your group<br />
#Type `groups` to see which groups you are part of<br />
newgrp <<YOUR GROUP ID>> <br />
<br />
<br />
<br />
== SAM MEG Data Analysis ==<br />
module load afni <br />
module load ctf<br />
module load samsrcv3/20180713-c5e1042<br />
<br />
== MNE python data analysis ==<br />
===To Access Additional MEG modules===<br />
#Add the following line to your ${HOME}/.bashrc<br />
module use --append /data/MEGmodules/modulefiles<br />
<br />
===Load MNE modules===<br />
#The module will not load on the biowulf head-node because freesurfer loads<br />
#Create an sinteractive or spersist node - adjust memory and cpus core number accordingly<br />
sinteractive --mem=6G --cpus-per-task=4 <br />
module load mne/0.24.1 # OR module load mne <<-- defaults to most current version<br />
<br />
ipython<br />
import mne<br />
<br />
===Load Commandline MNE scripts for Processing Data===<br />
!Currently in Beta Testing!<br />
[stoutjd@cn1023 modules]$ module list <br />
No modules loaded<br />
[stoutjd@cn1023 modules]$ module load mne_scripts<br />
[+] Loading freesurfer 7.1.1 on cn1023 <br />
[+] Loading mne 0.24.1 ... <br />
[+] Loading mne_scripts 0.1_dev ... <br />
Available:<br />
spatiotemporal_clustering_stats.py<br />
[stoutjd@cn1023 modules]$ spatiotemporal_clustering_stats.py -h <br />
usage: spatiotemporal_clustering_stats.py [-h] [-topdir TOPDIR] [-search SEARCH]<br />
[-outfname OUTFNAME]<br />
[-subjects_dir SUBJECTS_DIR]<br />
<br />
options:<br />
-h, --help show this help message and exit<br />
-topdir TOPDIR The directory w/ stc files<br />
-search SEARCH The search term to find the specific stc files for clustering<br />
-outfname OUTFNAME Output filename for the cluster nifti file<br />
-subjects_dir SUBJECTS_DIR<br />
Freesurfer subjects dir. Will download freesurfer average if not<br />
already present. Defaults to os.environ['SUBJECTS_DIR'] if not<br />
provided<br />
<br />
===MNE bids creation and MNE bids pipeline processing on biowulf===<br />
====Start interactive session with scratch to render visualization offscreen====<br />
sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50<br />
<br />
====Create BIDS data from data off the scanner====<br />
module load mne_scripts<br />
make_meg_bids.py -meg_input_dir MEGFOLDER -mri_brik AFNI_COREGED+orig.BRIK<br />
<br />
====Process data using MNE Bids Pipeline====<br />
module purge <br />
module load mne_bids_pipeline<br />
mne-bids-pipeline-run.py --config=CONFIG.py ##Optional --steps=preprocessing,source --subject=SUBJECTID(without sub-)<br />
<br />
==Best Practices for Group Data Preprocessing==<br />
===Process your project data===<br />
====Make your python script commandline callable====<br />
#It is typical to run 1 subject per commandline call and to parrallelize over subjects in the swarm file<br />
-Use [https://docs.python.org/3/library/argparse.html argpase] to manually build a full commandline call with keyword inputs and function description <br />
-Use [https://google.github.io/python-fire/guide/ fire] or [https://click.palletsprojects.com/en/8.0.x/ click] to automatically create a commandline call based on function inputs<br />
-Use sys.argv[] to create a simple commandline input (sys.argv[0] is the filename - argv[1] is the first argument - argv[2] is second...)<br />
<br />
Helpful Hints: <br />
-Use the meg dataset as an input, inside the python module - use the meg dataset to extract the subject ID :<br />
filename = os.path.basename(meg_dataset) <br />
subjid = filename.split('_')[0] OR if you have a custom ID subjid = filename[0:#characters]<br />
-Build output filenames using f-strings: <br />
outfile_base = f'{subjid}_{taskname}.nii'<br />
outfilename = os.path.join(outdir, outfile_base)<br />
<br />
====Build, test, and submit your swarm file====<br />
for i in ${GROUP_FOLDER}/*.ds; do echo my_process.py -in1 input1 -in2 -input2 -dataset $i >> swarm_file_preprocess.sh ; done<br />
<br />
#Make sure the process runs on at least one subject/dataset<br />
#This will run the last line of the swarmfile<br />
$(tail -1 ./swarm_file_preprocess.sh) <br />
<br />
#Verify the results on the single subject / possibly look at how much RAM / CPU was used before submitting the full batch to swarm<br />
swarm -f ./swarm_file_preprocess.sh -g ${GigsOfRAM} -t ${CPUcores} # -b ${How many subjects to run in row on 1 computer} - can be useful if you have a fast process<br />
<br />
== ADVANCED: Making your own python module ==<br />
=== Build the python conda environment ===<br />
It is recommended to create an install script so that this can be sent to a slurm job<br />
# Load conda - if set up according to the HPC page, this should work<br />
source /data/${USER}/conda/etc/profile.d/conda.sh; conda activate base<br />
<br />
# echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1 -y > installFile.sh<br />
# Make sure to include the -y or the job will hang waiting for user response<br />
# Also make sure you have an active conda prompt when submitting the swarm, or else it will fail<br />
echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y > python_install.sh<br />
swarm -f ./python_install.sh -g 4 -t 4<br />
=== Make a module file ===<br />
To display most of the contents of a module file run <br />
module display python #For the python module<br />
Output:<br />
----------------------------------------------------------------------------------<br />
/usr/local/lmod/modulefiles/python/3.8.lua:<br />
----------------------------------------------------------------------------------<br />
family("python")<br />
prepend_path("PATH","/usr/local/Anaconda/envs/py3.8/bin")<br />
pushenv("OMP_NUM_THREADS","1")<br />
Copy Template to your module folder<br />
#MyModule is the family name of the code / ${Version}.lua<br />
cp /usr/local/lmod/modulefiles/python/3.8.lua ${myModuleFilesDir}/${MyModule}/0.1.lua<br />
<br />
=== Add module files to the search path ===<br />
module use --append ${PathToUserModuleFiles}<br />
<br />
=== Final Step Load Your Module ===<br />
# !! The module load process does not give good feedback that it doesn't load - make sure the path in lua file is correct !!<br />
module load ${MyModuleName}<br />
<br />
#Example<br />
[$USERd@$NODE python_modules]$ module load mne<br />
<br />
[$USERd@$NODE python_modules]$ ipython<br />
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11) <br />
Type 'copyright', 'credits' or 'license' for more information<br />
IPython 8.1.1 -- An enhanced Interactive Python. Type '?' for help.<br />
<br />
In [1]: import mne<br />
<br />
In [2]: mne.__path__<br />
Out[2]: ['/data/ML_MEG/python_modules/mne0.24.1/lib/python3.9/site-packages/mne']</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_analysis_on_Biowulf&diff=5568MEG analysis on Biowulf2024-01-26T15:47:40Z<p>Jstout: </p>
<hr />
<div>== Biowulf brief intro ==<br />
Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br><br />
#For processing of data - reserve an sinteractive session<br />
sinteractive --mem=6G --cpus-per-task=4<br />
<br />
#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option<br />
Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br><br />
#Use scp for transfer or rsync -av (slower but some benefits)<br />
scp -r ./my_local_results ${USERNAME}@helix.nih.gov:/data/mydatafolder/.... <br />
<br />
#Getting results from biowulf cluster<br />
scp -r ${USERNAME}@helix.nih.gov:/data/mydatafolder/... ${PATH_OFSTUFF}/my_local_stuff<br />
<br />
Analysis of data should not be performed on the biowulf head node, but run through an sinteractive node or swarm process. <br><br />
To start with, there are a limited number of commands loaded on the system. To access more programs use module load. To search, use module spider.<br />
e.g. module load afni<br />
<br />
== Configuring your bash shell environment ==<br />
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.<br />
=== Edit .bashrc file in your home drive ===<br />
umask 002 #Gives automatic group permissions -- very very helpful for working with your team<br />
<br />
## Set up some aliases, so you don't have to type these out<br />
alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'<br />
alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'<br />
alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'<br />
<br />
=== Edit .bash_profile in your home drive ===<br />
#Set your default group (normally your default is your userID - which isn't helpful for your group<br />
#Type `groups` to see which groups you are part of<br />
newgrp <<YOUR GROUP ID>> <br />
<br />
<br />
<br />
== SAM MEG Data Analysis ==<br />
module load afni <br />
module load ctf<br />
module load samsrcv3/20180713-c5e1042<br />
<br />
== MNE python data analysis ==<br />
===To Access Additional MEG modules===<br />
#Add the following line to your ${HOME}/.bashrc<br />
module use --append /data/MEGmodules/modulefiles<br />
<br />
===Load MNE modules===<br />
#The module will not load on the biowulf head-node because freesurfer loads<br />
#Create an sinteractive or spersist node - adjust memory and cpus core number accordingly<br />
sinteractive --mem=6G --cpus-per-task=4 <br />
module load mne/0.24.1 # OR module load mne <<-- defaults to most current version<br />
<br />
ipython<br />
import mne<br />
<br />
===Load Commandline MNE scripts for Processing Data===<br />
!Currently in Beta Testing!<br />
[stoutjd@cn1023 modules]$ module list <br />
No modules loaded<br />
[stoutjd@cn1023 modules]$ module load mne_scripts<br />
[+] Loading freesurfer 7.1.1 on cn1023 <br />
[+] Loading mne 0.24.1 ... <br />
[+] Loading mne_scripts 0.1_dev ... <br />
Available:<br />
spatiotemporal_clustering_stats.py<br />
[stoutjd@cn1023 modules]$ spatiotemporal_clustering_stats.py -h <br />
usage: spatiotemporal_clustering_stats.py [-h] [-topdir TOPDIR] [-search SEARCH]<br />
[-outfname OUTFNAME]<br />
[-subjects_dir SUBJECTS_DIR]<br />
<br />
options:<br />
-h, --help show this help message and exit<br />
-topdir TOPDIR The directory w/ stc files<br />
-search SEARCH The search term to find the specific stc files for clustering<br />
-outfname OUTFNAME Output filename for the cluster nifti file<br />
-subjects_dir SUBJECTS_DIR<br />
Freesurfer subjects dir. Will download freesurfer average if not<br />
already present. Defaults to os.environ['SUBJECTS_DIR'] if not<br />
provided<br />
<br />
===MNE bids creation and MNE bids pipeline processing on biowulf===<br />
====Start interactive session with scratch to render visualization offscreen====<br />
sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50<br />
<br />
====Create BIDS data from data off the scanner====<br />
module load mne_scripts<br />
make_meg_bids.py -meg_input_dir MEGFOLDER -mri_brik AFNI_COREGED+orig.BRIK<br />
<br />
====Process data using MNE Bids Pipeline====<br />
module purge <br />
module load mne_bids_pipeline<br />
mne-bids-pipeline-run.py --config=CONFIG.py ##Optional --steps=preprocessing,source --subject=SUBJECTID(without sub-)<br />
<br />
==Best Practices for Group Data Preprocessing==<br />
===Process your project data===<br />
====Make your python script commandline callable====<br />
#It is typical to run 1 subject per commandline call and to parrallelize over subjects in the swarm file<br />
-Use [https://docs.python.org/3/library/argparse.html argpase] to manually build a full commandline call with keyword inputs and function description <br />
-Use [https://google.github.io/python-fire/guide/ fire] or [https://click.palletsprojects.com/en/8.0.x/ click] to automatically create a commandline call based on function inputs<br />
-Use sys.argv[] to create a simple commandline input (sys.argv[0] is the filename - argv[1] is the first argument - argv[2] is second...)<br />
<br />
Helpful Hints: <br />
-Use the meg dataset as an input, inside the python module - use the meg dataset to extract the subject ID :<br />
filename = os.path.basename(meg_dataset) <br />
subjid = filename.split('_')[0] OR if you have a custom ID subjid = filename[0:#characters]<br />
-Build output filenames using f-strings: <br />
outfile_base = f'{subjid}_{taskname}.nii'<br />
outfilename = os.path.join(outdir, outfile_base)<br />
<br />
====Build, test, and submit your swarm file====<br />
for i in ${GROUP_FOLDER}/*.ds; do echo my_process.py -in1 input1 -in2 -input2 -dataset $i >> swarm_file_preprocess.sh ; done<br />
<br />
#Make sure the process runs on at least one subject/dataset<br />
#This will run the last line of the swarmfile<br />
$(tail -1 ./swarm_file_preprocess.sh) <br />
<br />
#Verify the results on the single subject / possibly look at how much RAM / CPU was used before submitting the full batch to swarm<br />
swarm -f ./swarm_file_preprocess.sh -g ${GigsOfRAM} -t ${CPUcores} # -b ${How many subjects to run in row on 1 computer} - can be useful if you have a fast process<br />
<br />
== ADVANCED: Making your own python module ==<br />
=== Build the python conda environment ===<br />
It is recommended to create an install script so that this can be sent to a slurm job<br />
# Load conda - if set up according to the HPC page, this should work<br />
source /data/${USER}/conda/etc/profile.d/conda.sh; conda activate base<br />
<br />
# echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1 -y > installFile.sh<br />
# Make sure to include the -y or the job will hang waiting for user response<br />
# Also make sure you have an active conda prompt when submitting the swarm, or else it will fail<br />
echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y > python_install.sh<br />
swarm -f ./python_install.sh -g 4 -t 4<br />
=== Make a module file ===<br />
To display most of the contents of a module file run <br />
module display python #For the python module<br />
Output:<br />
----------------------------------------------------------------------------------<br />
/usr/local/lmod/modulefiles/python/3.8.lua:<br />
----------------------------------------------------------------------------------<br />
family("python")<br />
prepend_path("PATH","/usr/local/Anaconda/envs/py3.8/bin")<br />
pushenv("OMP_NUM_THREADS","1")<br />
Copy Template to your module folder<br />
#MyModule is the family name of the code / ${Version}.lua<br />
cp /usr/local/lmod/modulefiles/python/3.8.lua ${myModuleFilesDir}/${MyModule}/0.1.lua<br />
<br />
=== Add module files to the search path ===<br />
module use --append ${PathToUserModuleFiles}<br />
<br />
=== Final Step Load Your Module ===<br />
# !! The module load process does not give good feedback that it doesn't load - make sure the path in lua file is correct !!<br />
module load ${MyModuleName}<br />
<br />
#Example<br />
[$USERd@$NODE python_modules]$ module load mne<br />
<br />
[$USERd@$NODE python_modules]$ ipython<br />
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11) <br />
Type 'copyright', 'credits' or 'license' for more information<br />
IPython 8.1.1 -- An enhanced Interactive Python. Type '?' for help.<br />
<br />
In [1]: import mne<br />
<br />
In [2]: mne.__path__<br />
Out[2]: ['/data/ML_MEG/python_modules/mne0.24.1/lib/python3.9/site-packages/mne']</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5567Club MEG2024-01-24T17:00:38Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/26/2024 at 1:00pm''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''02/23/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5566Club MEG2024-01-23T19:14:35Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/26/2024 at 1:00pm''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5565Club MEG2024-01-23T19:14:02Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/26/2024''' Megan Parker - A smartphone delivered attention retraining intervention for altering neural underpinnings of food attention bias in adolescent girls with overweight or obesity<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5564Club MEG2023-12-12T21:12:08Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''--/--/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/26/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5560Club MEG2023-11-14T16:19:31Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5539Club MEG2023-10-23T15:10:55Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''10/20/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5538Club MEG2023-10-17T15:44:09Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
*** [https://www.jneurosci.org/content/jneuro/42/47/8807.full.pdf Whole-Brain Propagation Delays in Multiple Sclerosis, a Combined Tractography-Magnetoencephalography Study]<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5537Club MEG2023-10-16T17:52:03Z<p>Jstout: /* Recent Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Code: Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5536Club MEG2023-10-16T17:51:25Z<p>Jstout: /* Recent Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
** [https://github.com/nih-megcore/MEG_workshop_2023 Course Github Page]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5535Club MEG2023-10-16T17:50:11Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5534Club MEG2023-10-16T17:48:18Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
*** [https://www.sciencedirect.com/science/article/pii/S138824572300737X?casa_token=lP2ya9xhlBQAAAAA:7vx20m6eqPwKvc90PtswFxeZaVrYEklGAMg46guMAzy5fb_uDtMkA-HhcZAftdmFI6I2wQ Language MEG predicts postoperative verbal memory change in left mesial temporal lobe epilepsy]<br />
** Pei Robins<br />
** Amy Xu<br />
*** [https://www.sciencedirect.com/science/article/pii/S0165032722011405?via%3Dihub Convergent and divergent cognitive impairment of unipolar and bipolar depression: A magnetoencephalography resting-state study]<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_training_course_2023&diff=5532MEG training course 20232023-10-05T18:25:51Z<p>Jstout: /* Course Schedule and Material */</p>
<hr />
<div>!!!Under Construction!!!<br />
== Dates: ==<br />
'''Wednesday 09/27/2023 & Wednesday 10/04/2023'''<br />
<br />
This is a ''two day course''. Day 2 will build on the material and concepts covered on Day 1, so please plan to attend both days.<br />
<br />
== Location: ==<br />
FAES classroom <br><br />
Building 10 - Rooms 1&2<br />
<br />
==== Directions to the FAES Classrooms ====<br />
<br />
From Masur Auditorium, go north, past the Main Elevators. Look for the bookstore/coffee shop on your right and a sign from the ceiling saying "FAES Academic Center." Take a right down the hallway, through the double-door; then take the steps down to the lower level. <br />
<br />
====Wheelchair Access via Main elevator:====<br />
<br />
Take the Main Elevators outside Masur to the B1 level. Follow the "FAES Academic Center" signs down the hallway towards the Post Office. Across from the Post Office, enter the FAES Academic Center on the left. <br />
<br />
== Course Schedule and Material ==<br />
https://github.com/nih-megcore/MEG_workshop_2023<br />
<br />
== Things to do before the course ==<br />
Install the required installations for your computer (see below) <br><br />
Get a biowulf account:<br />
Full Link: https://hpc.nih.gov/docs/accounts.html <br />
Direct Link: https://hpcnihapps.cit.nih.gov/auth/accounts/account_request.php<br />
Confirm that you can log into biowulf with a terminal (mac / linux) or powershell (windows) after account approval!!<br />
<br />
== Required Installs: ==<br />
SSH terminal:<br />
Windows: powershell (included) or [https://mobaxterm.mobatek.net/download.html MobaXterm](Windows)<br />
Mac : terminal (included)<br />
Linux : terminal (included)<br />
<br />
== Recommended Installs: ==<br />
NoMachine:<br />
ALL: https://www.nomachine.com/<br />
<br />
Afni: <br />
ALL: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html<br />
<br />
freesurfer:<br />
#Download and sign up for a free license<br />
Windows: None<br />
Mac: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
Linux: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
<br />
Miniconda (NOT ANACONDA):<br />
#Find your operating system and run (possibly in a terminal)<br />
ALL: https://docs.conda.io/en/latest/miniconda.html<br />
<br />
Git:<br />
Windows: https://github.com/git-for-windows/git/releases/tag/v2.41.0.windows.3<br />
Mac: Have Xcode installed on system or https://git-scm.com/download/mac<br />
Linux: (ubuntu: sudo apt-get install git) (redhat: sudo dnf install git)<br />
<br />
== Format: ==<br />
----<br />
<br />
== Directions for Non-NIH Participants ==<br />
<br />
==== Security ====<br />
<br />
*[https://www.nih.gov/about-nih/visitor-information NIH Visitor Information]<br />
*[https://www.nih.gov/about-nih/visitor-information/campus-access-security Campus Access and Security]<br />
Please allow adequate time to get to the NIH main campus and to get through security (allow 30 minutes for security during peak commute hours). You will need to obtain a visitor's badge, so please bring a valid government-issued photo ID. Full requirements can be found at the link above.<br />
<br />
==== Navigating the NIH Campus ====<br />
<br />
Once you obtain your visitor's badge, proceed to your left, up the stairs or elevator to the upper level exit of the Visitor’s Center.<br />
<br />
The MEG Course will be held in Building 10 (the NIH Clinical Center), in FAES Classrooms 1 & 2.<br />
<br />
Take the NIH "Limited" Campus [https://wttsshuttle.com/map Shuttle] to Building 10, the NIH Clinical Center. Leave the shuttle at the building's South Entrance. Upon entering Building 10, follow the signs to Masur Auditorium. See directions from Masur Auditorium to the FAES Classrooms above.</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5531Club MEG2023-10-05T18:13:14Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Amy Xu<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus) - https://megcore.nih.gov/index.php/MEG_North_America_Workshop<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5523Club MEG2023-09-26T17:42:53Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Amy Xu<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus)<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_training_course_2023&diff=5522MEG training course 20232023-09-22T17:15:38Z<p>Jstout: </p>
<hr />
<div>!!!Under Construction!!!<br />
== Dates: ==<br />
'''Wednesday 09/27/2023 & Wednesday 10/04/2023'''<br />
<br />
This is a ''two day course''. Day 2 will build on the material and concepts covered on Day 1, so please plan to attend both days.<br />
<br />
== Location: ==<br />
FAES classroom <br><br />
Building 10 - Rooms 1&2<br />
<br />
==== Directions to the FAES Classrooms ====<br />
<br />
From Masur Auditorium, go north, past the Main Elevators. Look for the bookstore/coffee shop on your right and a sign from the ceiling saying "FAES Academic Center." Take a right down the hallway, through the double-door; then take the steps down to the lower level. <br />
<br />
====Wheelchair Access via Main elevator:====<br />
<br />
Take the Main Elevators outside Masur to the B1 level. Follow the "FAES Academic Center" signs down the hallway towards the Post Office. Across from the Post Office, enter the FAES Academic Center on the left. <br />
<br />
== Course Schedule and Material ==<br />
(Will be under construction until Wed-27th) https://github.com/nih-megcore/MEG_workshop_2023<br />
<br />
== Things to do before the course ==<br />
Install the required installations for your computer (see below) <br><br />
Get a biowulf account:<br />
Full Link: https://hpc.nih.gov/docs/accounts.html <br />
Direct Link: https://hpcnihapps.cit.nih.gov/auth/accounts/account_request.php<br />
Confirm that you can log into biowulf with a terminal (mac / linux) or powershell (windows) after account approval!!<br />
<br />
== Required Installs: ==<br />
SSH terminal:<br />
Windows: powershell (included) or [https://mobaxterm.mobatek.net/download.html MobaXterm](Windows)<br />
Mac : terminal (included)<br />
Linux : terminal (included)<br />
<br />
== Recommended Installs: ==<br />
NoMachine:<br />
ALL: https://www.nomachine.com/<br />
<br />
Afni: <br />
ALL: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html<br />
<br />
freesurfer:<br />
#Download and sign up for a free license<br />
Windows: None<br />
Mac: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
Linux: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
<br />
Miniconda (NOT ANACONDA):<br />
#Find your operating system and run (possibly in a terminal)<br />
ALL: https://docs.conda.io/en/latest/miniconda.html<br />
<br />
Git:<br />
Windows: https://github.com/git-for-windows/git/releases/tag/v2.41.0.windows.3<br />
Mac: Have Xcode installed on system or https://git-scm.com/download/mac<br />
Linux: (ubuntu: sudo apt-get install git) (redhat: sudo dnf install git)<br />
<br />
== Format: ==<br />
----<br />
<br />
== Directions for Non-NIH Participants ==<br />
<br />
==== Security ====<br />
<br />
*[https://www.nih.gov/about-nih/visitor-information NIH Visitor Information]<br />
*[https://www.nih.gov/about-nih/visitor-information/campus-access-security Campus Access and Security]<br />
Please allow adequate time to get to the NIH main campus and to get through security (allow 30 minutes for security during peak commute hours). You will need to obtain a visitor's badge, so please bring a valid government-issued photo ID. Full requirements can be found at the link above.<br />
<br />
==== Navigating the NIH Campus ====<br />
<br />
Once you obtain your visitor's badge, proceed to your left, up the stairs or elevator to the upper level exit of the Visitor’s Center.<br />
<br />
The MEG Course will be held in Building 10 (the NIH Clinical Center), in FAES Classrooms 1 & 2.<br />
<br />
Take the NIH "Limited" Campus [https://wttsshuttle.com/map Shuttle] to Building 10, the NIH Clinical Center. Leave the shuttle at the building's South Entrance. Upon entering Building 10, follow the signs to Masur Auditorium. See directions from Masur Auditorium to the FAES Classrooms above.</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_training_course_2023&diff=5521MEG training course 20232023-09-21T20:29:47Z<p>Jstout: /* Course Schedule and Material */</p>
<hr />
<div>!!!Under Construction!!!<br />
== Dates: ==<br />
'''Wednesday 09/27/2023 & Wednesday 10/04/2023'''<br />
<br />
This is a ''two day course''. Day 2 will build on the material and concepts covered on Day 1, so please plan to attend both days.<br />
<br />
== Location: ==<br />
FAES classroom <br><br />
Building 10 - Rooms 1&2<br />
<br />
==== Directions to the FAES Classrooms ====<br />
<br />
From Masur Auditorium, go north, past the Main Elevators. Look for the bookstore/coffee shop on your right and a sign from the ceiling saying "FAES Academic Center." Take a right down the hallway, through the double-door; then take the steps down to the lower level. <br />
<br />
====Wheelchair Access via Main elevator:====<br />
<br />
Take the Main Elevators outside Masur to the B1 level. Follow the "FAES Academic Center" signs down the hallway towards the Post Office. Across from the Post Office, enter the FAES Academic Center on the left. <br />
<br />
== Course Schedule and Material ==<br />
(Will be under construction until Wed-27th) https://github.com/nih-megcore/MEG_workshop_2023<br />
<br />
== Things to do before the course ==<br />
Install the required installations for your computer (see below) <br><br />
Get a biowulf account:<br />
Full Link: https://hpc.nih.gov/docs/accounts.html <br />
Direct Link: https://hpcnihapps.cit.nih.gov/auth/accounts/account_request.php<br />
Confirm that you can log into biowulf with a terminal (mac / linux) or powershell (windows) after account approval!!<br />
<br />
== Required Installs: ==<br />
SSH terminal:<br />
Windows: powershell (included) or [https://mobaxterm.mobatek.net/download.html MobaXterm](Windows)<br />
Mac : terminal (included)<br />
Linux : terminal (included)<br />
<br />
NoMachine:<br />
ALL: https://www.nomachine.com/<br />
<br />
== Recommended Installs: ==<br />
Afni: <br />
ALL: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html<br />
<br />
freesurfer:<br />
#Download and sign up for a free license<br />
Windows: None<br />
Mac: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
Linux: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
<br />
Miniconda (NOT ANACONDA):<br />
#Find your operating system and run (possibly in a terminal)<br />
ALL: https://docs.conda.io/en/latest/miniconda.html<br />
<br />
Git:<br />
Windows: https://github.com/git-for-windows/git/releases/tag/v2.41.0.windows.3<br />
Mac: Have Xcode installed on system or https://git-scm.com/download/mac<br />
Linux: (ubuntu: sudo apt-get install git) (redhat: sudo dnf install git)<br />
<br />
== Format: ==<br />
----<br />
<br />
== Directions for Non-NIH Participants ==<br />
<br />
==== Security ====<br />
<br />
*[https://www.nih.gov/about-nih/visitor-information NIH Visitor Information]<br />
*[https://www.nih.gov/about-nih/visitor-information/campus-access-security Campus Access and Security]<br />
Please allow adequate time to get to the NIH main campus and to get through security (allow 30 minutes for security during peak commute hours). You will need to obtain a visitor's badge, so please bring a valid government-issued photo ID. Full requirements can be found at the link above.<br />
<br />
==== Navigating the NIH Campus ====<br />
<br />
Once you obtain your visitor's badge, proceed to your left, up the stairs or elevator to the upper level exit of the Visitor’s Center.<br />
<br />
The MEG Course will be held in Building 10 (the NIH Clinical Center), in FAES Classrooms 1 & 2.<br />
<br />
Take the NIH "Limited" Campus [https://wttsshuttle.com/map Shuttle] to Building 10, the NIH Clinical Center. Leave the shuttle at the building's South Entrance. Upon entering Building 10, follow the signs to Masur Auditorium. See directions from Masur Auditorium to the FAES Classrooms above.</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5516Club MEG2023-09-19T16:40:03Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/20 or 09/22''' Basic computing primer: Intro to Linux / Bash / Python / Biowulf <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Amy Xu<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus)<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
* '''03/--/2024''' Possibly DC Brainhack<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5509Club MEG2023-09-12T19:35:25Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/20 or 09/22''' Basic computing primer: Intro to Linux / Bash / Python / Biowulf <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Amy Xu<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus)<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=MEG_training_course_2023&diff=5508MEG training course 20232023-09-12T18:25:00Z<p>Jstout: </p>
<hr />
<div>!!!Under Construction!!!<br />
== Dates: ==<br />
09/27/2023 & 10/04/2023<br />
<br />
== Location: ==<br />
FAES classroom <br><br />
Building 10 - Rooms 1&2<br />
<br />
== Course Schedule and Material ==<br />
(This will open up shortly before the course) https://github.com/nih-megcore/MEG_workshop_2023<br />
<br />
== Things to do before the course ==<br />
Install the required installations for your computer (see below) <br><br />
Get a biowulf account:<br />
Full Link: https://hpc.nih.gov/docs/accounts.html <br />
Direct Link: https://hpcnihapps.cit.nih.gov/auth/accounts/account_request.php<br />
Confirm that you can log into biowulf with a terminal (mac / linux) or powershell (windows) after account approval!!<br />
<br />
== Required Installs: ==<br />
SSH terminal:<br />
Windows: powershell (included) or [https://mobaxterm.mobatek.net/download.html MobaXterm](Windows)<br />
Mac : terminal (included)<br />
Linux : terminal (included)<br />
<br />
NoMachine:<br />
ALL: https://www.nomachine.com/<br />
<br />
== Recommended Installs: ==<br />
Afni: <br />
ALL: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html<br />
<br />
freesurfer:<br />
#Download and sign up for a free license<br />
Windows: None<br />
Mac: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
Linux: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall<br />
<br />
Miniconda (NOT ANACONDA):<br />
#Find your operating system and run (possibly in a terminal)<br />
ALL: https://docs.conda.io/en/latest/miniconda.html<br />
<br />
Git:<br />
Windows: https://github.com/git-for-windows/git/releases/tag/v2.41.0.windows.3<br />
Mac: Have Xcode installed on system or https://git-scm.com/download/mac<br />
Linux: (ubuntu: sudo apt-get install git) (redhat: sudo dnf install git)<br />
<br />
== Format: ==<br />
----</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5498Club MEG2023-08-30T01:45:04Z<p>Jstout: </p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''09/20 or 09/22''' Basic computing primer: Intro to Linux / Bash / Python / Biowulf <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' <br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Paul Rohde<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus)<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/18/2023''' Arshitha Basavaraj and Jeff Stout - Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstouthttps://megcore.nih.gov/index.php?title=Club_MEG&diff=5486Club MEG2023-08-15T15:41:14Z<p>Jstout: /* Upcoming Talks/Discussions */</p>
<hr />
<div>Club MEG is our version of a journal club. We welcome NIH MEG researchers to lead discussions on any MEG topic, including interesting papers, experiment ideas, analysis techniques, or finding from your research.<br />
<br />
Interested in presenting a topic? Email '''Fred Carver at carverf@nih.gov''' or '''Jeff Stout at stoutjd@nih.gov''' if you would like to present.<br />
<br />
Notifications of upcoming talks are sent to the [https://list.nih.gov/cgi-bin/wa.exe?A0=meg_announce MEG_ANNOUNCE (NIH MEG Core Users only)] and [https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLUB-MEG_ANNOUNCE&A=1 Club-MEG_ANNOUNCE] listservs.<br />
<br />
<br />
== Upcoming Talks/Discussions == <br />
* '''08/18/2023 at 1:00pm''' Club MEG: Arshitha Basavaraj and Jeff Stout - ''Curating / Uploading / Editing / Versioning MEG BIDS data for OpenNeuro''<br />
* '''09/20 or 09/22''' Basic computing primer: Intro to Linux / Bash / Python / Biowulf <br />
* '''09/27(Wednesday) & 10/04/2023(Wednesday)''' MEG training course part1<br />
** [https://megcore.nih.gov/index.php/MEG_training_course_2023 MEG Training Course]<br />
* '''10/16-10/19/23''' - CuttingGardens: (CuttingEEG group) - https://cuttinggardens2023.org<br />
* '''10/20/2023 at 1:00pm''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
** Elena Hayday<br />
** Pei Robins<br />
** Paul Rohde<br />
* '''11/08/2023-11/09/2023''' MEG North America (at NIH campus)<br />
* '''12/15/2023 at 1:00pm''' Shivam Bansal - Naturalistic Stimuli MEG Analysis<br />
* '''01/12/2024''' Megan Parker<br />
* '''02/09/2024''' Yoojin Lee<br />
<br />
== Recent Talks/Discussions ==<br />
* '''08/04/2023''' Sue Tong and Daniel Eisenberg - Schizophrenia, antipsychotic treatment, and cortical function<br />
* '''07/28/2023''' Riley Hochstein - Magnetocardiography with OPMs<br />
* '''06/30/2023''' Club MEG: (Multi-Presenter: 3x 15min talks)<br />
**Sebastian Montesinos<br />
***[https://elifesciences.org/articles/33904 Differential temporal dynamics during visual imagery and perception] <br />
**Miguel Jaime<br />
***[https://molecularautism.biomedcentral.com/articles/10.1186/s13229-022-00498-2 Globally elevated excitation–inhibition ratio in children with autism spectrum disorder and below-average intelligence]<br />
**Bess Bloomer<br />
***[https://www.sciencedirect.com/science/article/pii/S2213158223000530 Functional connectivity changes during working memory in autism spectrum disorder: A two-year longitudinal MEG study]<br />
* '''05/19/2023''' Club MEG: (Multi-Presenter: 3X 15min talks)<br />
**Angela Wang<br />
***[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342265/ Localization of Early-Stage Visual Processing Deficits at Schizophrenia Spectrum Illness Onset Using Magnetoencephalography ] <br />
**Price Withers<br />
***[https://www.sciencedirect.com/science/article/pii/S1053811921002007?via%3Dihub Dynamic analysis on simultaneous iEEG-MEG data via hidden Markov model]<br />
**Kaya Scheman<br />
***[https://www.sciencedirect.com/science/article/pii/S138824571830261X Advanced dynamic statistical parametric mapping with MEG in localizing epileptogenicity of the bottom of sulcus dysplasia]<br />
* '''05/12/2023''' Christian Brodbeck (University of Connecticut) - Eelbrain Software Demonstration (for neurophysiological statistics)<br />
**https://eelbrain.readthedocs.io/en/r-0.27/index.html<br />
* '''05/05/2023''' -- [https://megcore.nih.gov/index.php/MEG_Hackathon_2023 '''MEG Hackathon 2023''']<br />
** [https://github.com/nih-megcore/MEGHACK_2023_spring GitHub_Repos]<br />
* '''04/28/2023 at 1:00pm''' Club MEG: Abbas Babajani-Feremi - (University of Florida) - ''MEG Presurgical Language Mapping Using a Novel Automatic Equivalent Current Dipole Algorithm (AsECDa) in Comparison with MNE, dSPM, and DICS Beamformer''<br />
**[https://megcore.nih.gov/MEG/AbbasBabajani-Feremi_ClubMEG_04282023.mp4 Recording Download (mp4)]<br />
* '''04/21/2023 at 1:00pm''' Hackathon Prep -- Go over ideas and best practices - setup git repos for the project.<br />
**[https://megcore.nih.gov/index.php/MEG_Hackathon_2023 MEG Hackathon 2023 -- SIGN UP!]<br />
* '''03/03/2023''' Graham Flick (New York University) - ''Visual word recognition in natural reading: A co-registered MEG and eye-tracking study''<br />
* '''02/24/2023''' Georgios Michalareas (Max Planck Institute) - [https://www.sciencedirect.com/science/article/pii/S0896627315011204?via%3Dihub Alpha-Beta and Gamma Rhythms Subserve Feedback and Feedforward Influences among Human Visual Cortical Areas]<br />
* '''02/03/2023''' Lina Teichman and Amaia Benitez Andonegui - The temporal evolution of colour-space geometries in the human brain<br />
* '''01/27/2023''' Lucrezia Liuzzi - Identifying markers of cognitive control<br />
* '''12/09/2022''' Ryan Oakeson and Amaia Benitez, [https://www.biorxiv.org/content/10.1101/2022.05.31.494173v3 Top-down information flow drives lexical access when listening to continuous speech]<br />
* '''12/02/2022''' Anna Namyst, [https://www.frontiersin.org/articles/10.3389/fpsyg.2016.00995/full Establishing New Mappings between Familiar Phones: Neural and Behavioral Evidence for Early Automatic Processing of Nonnative Contrasts]<br />
* '''10/28/2022''' - Sharif Kronemer - "The neural mechanisms of afterimages: A model of illusory conscious perception"<br />
**[https://megcore.nih.gov/MEG/SharifKronemer_ClubMEG_10282022.mp4 Recording Download (mp4)]<br />
* '''10/07/2022''' - Sarah Grewal - [https://pubs.rsna.org/doi/10.1148/radiol.212453 On-Scalp Optically Pumped Magnetometers versus Cryogenic Magnetoencephalography for Diagnostic Evaluation of Epilepsy in School-aged Children (Journal Article)] <br />
**[https://megcore.nih.gov/MEG/SarahGrewal_ClubMEG_10072022.mp4 Recording Download (mp4)]<br />
* '''09/16/2022''' Lindsay Oberman - Autism background, MEG autism biomarkers, interventional approach, and preliminary study results<br />
**[https://megcore.nih.gov/MEG/Oberman_ClubMEG_09162022.mp4 Recording Download (mp4)]<br />
** [https://pubmed.ncbi.nlm.nih.gov/25745372/ Prospective MEG biomarkers in ASD: pre-clinical evidence and clinical promise of electrophysiological signatures]<br />
* '''09/15/2022''' Biomag 2022 Recap<br />
* '''08/19/2022''' Kunjan Rana - Communication Between the Amygdala and Cortex in the Context of Face Processing<br />
**[https://megcore.nih.gov/MEG/KunjanRana_ClubMEG_08192022.mp4 Recording Download (mp4)]<br />
* '''08/05/2022''' Shruti Japee - Temporal Dynamics of Facial Expression Processing<br />
**[https://megcore.nih.gov/MEG/ShrutiJapee_ClubMEG_FacialExpressionDecoding_08052022.mp4 Recording Download (mp4)]<br />
* '''05/20/2022''' Priyanka Shah (Medical College of Wisconsin) - Resting Connectivity Changes in Temporal Lobe Epilepsy<br />
**[https://megcore.nih.gov/MEG/PriyankaShah-Basak_ClubMEG_05202022.mp4 Recording Download (mp4)]<br />
* '''05/13/2022''' Jess Gilbert - MEG Studies of Treatment-Resistant Depression and Ketamine Response<br />
**[https://megcore.nih.gov/MEG/JessGilbert_ClubMEG_05132022.mp4 Recording Download (mp4)]<br />
* '''04/29/2022''' Ethan Buch [https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay]<br />
** [https://megcore.nih.gov/MEG/EthanBuch_HumanSkill_ClubMEG_04292022.mp4 Recording Download (mp4)]<br />
* '''04/08/2022''' Allison Nugent [https://doi.org/10.1038/s42003-021-01785-z Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization]<br />
** [https://megcore.nih.gov/MEG/AllisonNugent_ClubMEGJournal_04082022.mp4 Recording Download (mp4)]<br />
* '''03/10/2022''' Stephen Robinson - Using Information Theory for MEG Studies<br />
** [https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Recording Download (mp4)]<br />
* '''02/11/2022''' Megan Parker - [https://www.sciencedirect.com/science/article/pii/S000689931301500X?via%3Dihub Neural regulatory mechanism of desire for food: revealed by magnetoencephalography (article)]<br />
* '''11/12/2021''' Amaia Benitez, From ECoG to Magnetocorticography: Optically Pumped Magnetometers for Non-Invasive, High Resolution Imaging<br />
** [https://megcore.nih.gov/MEG/ClubMEG_111221_AmaiaBenitez_OPMs&MCog.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:ClubMeg ABA OPMs 111221.pdf|OPM and MCog Research Introduction]]<br />
*'''10/22/2021''' Stephen Robinson, Fundamentals of Beamformers (mp4)<br />
** [https://megcore.nih.gov/MEG/ClubMEG_Robinson_Beamforming_10222021.mp4 Recording Download (mp4)]<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:StephenRobinson SAM Beamforming Talk 10222021.pdf|SAM Beamforming Fundamentals]]<br />
*'''10/23/2020''' Angela Wang and Tom Holroyd, Neurofeedback Discussion.<br />
**Slides: [[File:Pdf.png|PDF]] [[Media:Neurofeedback_Review.pdf|Neurofeedback Review]]; [[Media:RT-MEG.pdf|Real-time Beamforming]].<br />
<br />
== Previous Tutorials and Training ==<br />
* Jeff Stout (02/17/2023) - Making python modules<br />
**<br />
**[https://docs.python.org/3/distutils/setupscript.html Configuring a setup.py file ]<br />
* Jeff Stout (10/21/2022) - MNE_BIDS/MNE_BIDS_PIPELINE/Biowulf MEG Bids Modules<br />
**[https://megcore.nih.gov/MEG/Stout_MNE-BIDStutorial_10212022.mp4 Recording Download (mp4)]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_ClubMEG_bids_10212022.pdf Slides]<br />
**[[Image:pdf.png]] [https://megcore.nih.gov/MEG/Stout_mne-bids_example_use_10212022.pdf mne-bids example usage]<br />
**Additional Info (referenced in video): https://megcore.nih.gov/index.php/Mne_bids_pipeline<br />
* John Veillette, University of Chicago (10/14/2022) - MNE-ARI (All Resolutions Imaging) Theoretical Overview and Demo<br />
**https://github.com/john-veillette/mne-ari<br />
**[https://megcore.nih.gov/MEG/Veillette_MNE-ARI_ClubMEG_10142022.mp4 Recording Download (mp4)]<br />
* Tom Holroyd (09/30/2022) - Demonstration of SAM beamforming using Sequential Regression (SER) covariance updating for real-time analysis<br />
**[https://megcore.nih.gov/MEG/TomHolroyd_SAM-SER-RealtimeAnalysis_09302022.mp4 Recording Download (mp4)]<br />
* Anna Namyst and Jeff Stout (09/09/2022) - Eye Tracking Overview<br />
** [[Image:pdf.png]] https://jov.arvojournals.org/article.aspx?articleid=2772164<br />
** [[Image:pdf.png]] https://www.biorxiv.org/content/10.1101/2021.07.09.451139v1.full.pdf<br />
** [[Image:pdf.png]] [https://megcore.nih.gov/MEG/ClubMeg_EyeTracking_09092022.pdf Slides]<br />
* Group Session (08/12/2022) - Connectivity Coding Zoom Call [[Meg_information_based_connectivity_coding_session]]<br />
*Andrea Brovelli & Etienne Combrisson, Institut de Neurosciences de la Timone (07/13/2022) - FRITES Theoretical Overview and Demo (Connectivity Calculation and Stats)<br />
**[https://megcore.nih.gov/MEG/FRITES_Tutorial_07132022.mp4 Recording Download (mp4)]<br />
**[https://brainets.github.io/frites/ Website and Github Page] [https://github.com/brainets/CookingFrites Example Training Notebooks]<br />
**[https://doi.org/10.1016/j.neuroimage.2022.119347 Paper: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data]<br />
*[https://megcore.nih.gov/index.php?title=MEG_Hackathon_2022 MEG Hackathon ] 05/06/2022<br />
*Eric Earl (04/27/2022) - Github Presentation and Discussion <br />
**[https://docs.google.com/presentation/d/15l6Pb6pUICPSsJi3shWLiAJNlCkngHi0fzht7FKeyqM/edit?usp=sharing Presentation Slides] [https://slides.com/ericearl/gh-repo Advanced Github Features]<br />
** [https://megcore.nih.gov/MEG/EricEarl_ClubMEG_GitHubTutorial_04272022.mp4 Recording Download (mp4)]<br />
**Additional Links: <br />
***[https://osf.io/xt6pk/ ReadTheDocs] <br />
***[https://osf.io/qcyhu/ BioDataClub OSF] <br />
*Jeff Stout, Intro to Git, 04/12/2022 - <br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022.mp4 Recording Download]<br />
**[https://megcore.nih.gov/MEG/JeffStout_GitTutorial_04122022_commands.txt Git Tutorial Commands ]<br />
**Additional Links:<br />
***[https://nbviewer.org/github/pelson/lessons_for_a_scientific_programmer/blob/master/2014-euroscipy/00_intro.ipynb Scientific Programming Guidelines - Including Git]<br />
*Jeff Stout, Intro Python, 03/29/2022 - [https://megcore.nih.gov/MEG/JeffStout_PythonCoursePart2_03292022.mp4| Dictionaries/Functions/Scripts/Modules/commandline interface -- Recording Download (mp4)]<br />
*Fred Carver & Jeff Stout, [[Tutorial stats 011422| Tutorial Link]] (01/21/22) -- MEG Group Data Analysis in AFNI and MNE Python <br />
**[https://megcore.nih.gov/MEG/ClubMEG_Carver&Stout_MNE&AFNI-GroupAnalysisTutorial_012122.mp4 Recording Download (mp4)]<br />
*Jeff Stout, [[MNE Python Tutorial 2021]] -- Introduction to MEG processing with MNE Python<br />
*NIMH MEG Core Staff, [[NIH MEG Short Course 2018]] -- Useful training materials.<br />
<br />
== Special Interest Groups ==<br />
<br />
[https://megcore.nih.gov/index.php?title=Machine_Learning_SIG '''Machine Learning Special Interest Group'''] (ML SIG) - 4th Friday of every month 1-2pm. Contact Jeff Stout for more information on joining or presenting.</br><br />
'''''Prior ML SIG topics:'''''<br />
* '''05/27/2022''' Jeff Stout - [https://www.sciencedirect.com/science/article/pii/S1053811921006777 MEGnet: Automatic ICA-based artifact removal for MEG using spatiotemporal convolutional neural networks] <br />
**[https://megcore.nih.gov/MEG/JeffStout_MEGnetOverview_ML-SIG_05292022.mp4 Recording Download (mp4)]<br />
*'''04/15/2022''' Leonardo Claudino - Decoding Pipeline <ref> https://www.sciencedirect.com/science/article/pii/S2211124721005398?via%3Dihub Consolidation of human skill linked to waking hippocampo-neocortical replay Ethan R. Buch, Leonardo Claudino, Romain Quentin, Marlene Bönstrup, Leonardo Cohen</ref><ref>https://github.com/hcps-ninds/Replay ANALYSIS CODE: Consolidation of human skill linked to waking hippocampo-neocortical replay </ref> <br />
** [https://megcore.nih.gov/MEG/LeoClaudino_DecodingPipeline_MEG-ML-SIG_04152022.mp4 Recording Download (mp4)]<br />
*'''03/25/2022''' Mina Kheirkhah Rahimabadi - Classification of brain responses to emotional image stimuli measured with MEG<br />
*'''03/04/2022''' Dave Dash - Decoding speech with MEG <ref>Dash D, Ferrari P, Wang J. Decoding Imagined and Spoken Phrases From Non-invasive Neural (MEG) Signals. Front Neurosci. 2020;14:290. Published 2020 Apr 7. doi:10.3389/fnins.2020.00290</ref> <ref>Dash D, Wisler A, Ferrari P, Davenport EM, Maldjian J, Wang J. MEG Sensor Selection for Neural Speech Decoding. IEEE Access. 2020;8:182320-182337. doi:10.1109/access.2020.3028831</ref> <ref>Dash D, Ferrari P, Dutta S, Wang J. NeuroVAD: Real-Time Voice Activity Detection from Non-Invasive Neuromagnetic Signals. Sensors (Basel). 2020;20(8):2248. Published 2020 Apr 16. doi:10.3390/s20082248</ref> <br />
**[https://megcore.nih.gov/MEG/DebadattaDash_MEG-SpeechDecoding_ClubMEG_03042022.mp4 Recording Download (mp4)]<br />
*'''01/28/2022''' Lina Teichmann - Bayes Factors for Time-series Decoding<br />
**[https://megcore.nih.gov/MEG/Teichmann_MEGMachineLearningSIG_BayesFactorsTimeSeriesDecoding_01282022.mp4 Teichmann 01/28/22 Recording Download (mp4)]<br />
** Slides: [[File:Pdf.png|PDF]] [https://megcore.nih.gov/MEG/Teichmann_BayesFactors_ClubMEG_01282022.pdf Bayes Factors for Time-Series Decoding]<br />
** [https://www.biorxiv.org/content/10.1101/2021.06.23.449663v3.abstract Journal Article] and [https://github.com/LinaTeichmann1/BFF_repo Associated Code]<br />
*'''12/03/2021''' Initial meeting for Machine Learning in MEG SIG - Journal Club discussion: [https://pubmed.ncbi.nlm.nih.gov/28782682/ Deconstructing multivariate decoding for the study of brain function]<br />
<br />
==References==</div>Jstout