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UNDER CONSTRUCTION
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====Enigma Project - MEG working group====
The enigma project is a large scale neuroimaging project to leverage data across multiple institutes to identify neuroimaging findings that are generally not possible at a single institute. <br>
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http://enigma.ini.usc.edu/


====MEG Working group====


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[http://enigma.ini.usc.edu/ The ENIGMA Consortium]<br>
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====Data Analysis====
[http://enigma.ini.usc.edu/ongoing/enigma-meg-working-group/ The ENIGMA MEG Working Group]</br>


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==Enigma Project - MEG working group==
===Singularity Container===
The goal of the ENIGMA MEG Working Group is to explore the spatiotemporal patterns of brain oscillatory activity, and determine how these patterns relate to age, gender, and common genetic variants. Data from numerous modalities have demonstrated a hierarchical organization of the brain from sensory systems to higher cortical areas. There is some evidence that this hierarchical organization may also be reflected in the spatial distribution of intrinsic timescales of activity. This ENIGMA working group intends to explore these patterns across the lifespan. To achieve the highest possible number of subjects, this needs to be done by meta-analysis.<br>
Singularity is a container technology (similar to Docker). We are using containers to allow for easy distribution of the analysis pipeline and analysis consistency. Singularity was chosen becuase it does not require administrative priveledges during runtime and can be run on an HPC system. Being a container, the analysis can be run on any platform (linux, mac, windows, ...). <br>
https://sylabs.io/singularity/


[mailto:nugenta@nih.gov Allison Nugent, PhD], ENIGMA MEG Chair <br>
===Resting State Analysis===
[mailto:jeff.stout@nih.gov Jeff Stout, PhD], Lead Scientist <br>
The analysis routine has been implemented in MNE python (https://mne.tools/stable/index.html) and packaged into a singularity container. This guarantees that differences in software dependencies and operating system configurations have been eliminated.
[mailto:anna.namyst@nih.gov Anna Namyst, BA], Project Coordinator</br>


==MEG Working Group: Participating Institutions==
The singularity def file can be found at:
[[File:ENIGMA-MEG-WG 12.2021.jpg|frameless|right|500px|600px| Global Participation in the ENIGMA MEG Working Group]]
github.com/........ upload
* Advent Health for Children
* Arkansas Childrens Hospital
* Aston University, UK
* Cambridge University
* Children's Hospital of Philadephia
* DNISC (Università degli Studi G.D'Annunzio Chieti Pescara)
* IRCCS San Camillo Hospital Venice
* Johannes Gutenberg University, Mainz, Germany (Biomedical statistics and multimodal signal processing Unit)
* Macquarie University
* Massachusetts General Hospital
* McGill University, Montreal Neurological Institute
* National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
* Nemours DuPont Hospital for Children
* NeuroSpin
* New York University and NYU Abu Dhabi
* NIH/NICHD
* NIH/NIMH
* Precision Medicine Centre, Hokuto Hospital
* Precision Medicine Centre, Kumagaya General Hospital
* Salisbury VA Medical Center, Wake Forest University, Wake Forest School of Medecine
* The Mind Research Network
* Thomas Jefferson University
* Universiti Sains Malaysia
* Universiti Teknologi PETRONAS
* University of Alabama, Birmingham
* University of Göttingen
* University of Jyväskylä, Finland
* University of Pittsburgh
* University of Pittsburgh
* University of Texas Southwestern
* University of Tübingen


If you are interested in participating in this project, please email the project coordinator, [mailto:anna.namyst@nih.gov Anna Namyst], for more information.
The singularity container can be downloaded from:
Under Construction


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==Data Analysis==
Anatomical Preprocessing:
Data analysis will be available in two flavors:
Surface models: Scalp, Outer Skull, Inner Skull, Pial Surface
1. Upload coregistered anonymized data to NIH
Coregistration of the MRI and MEG data
2. Perform analysis at acquisition site using EnigmaMeg scripts
Parcel extraction (freesurfer autorecon3)
Subparcel calculation (mne ....)


*[https://github.com/jstout211/enigma_MEG ENIGMA MEG Pipeline on GitHub]
The resting state analysis steps:
*[https://megcore.nih.gov/index.php/ENIGMA_MEG_Pipeline_FAQ Processing Pipeline FAQ]
Check data type and load data
Downsample to 200Hz
Split to 1 second epochs
Reject sensor level data at a specific threshold
Calculate broad band dSPM inverse solution
Filter the data into bands (1-3, 3-6, 8-12, 13-35, 35-55)
Project the data to parcels and create parcel time series
Calculate relative power in each band and parcel


==Upload Data to be analyzed on NIH Biowulf cluster==
Outputs:
Instructions for data preparation and upload: <br>
The outputs of the analysis will result in a csv file
[https://megcore.nih.gov/index.php/ENIGMA_MEG_data_upload ENIGMA MEG Data Upload]
A csv file for each subject will be created in the subfolder of the singularity directory
A final command can be run to calculate the summary statistics
Submission of Results:
After calculating the local institutes summary statistics, the group csv file will be uploaded to the NIMH.


==Potential MEG Subanalyses==
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Meta-Analysis:
Healthy Volunteers
Statistics will be compiled across institutes
Epilepsy
Alzheimer's and dementia
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Motor Analysis
Language Processing
Anxiety Disorders
Schizophrenia and related disorders
Developmental disorders
Traumatic Brain Injury
Stroke

Latest revision as of 16:48, 14 February 2024


The ENIGMA Consortium
The ENIGMA MEG Working Group

Enigma Project - MEG working group

The goal of the ENIGMA MEG Working Group is to explore the spatiotemporal patterns of brain oscillatory activity, and determine how these patterns relate to age, gender, and common genetic variants. Data from numerous modalities have demonstrated a hierarchical organization of the brain from sensory systems to higher cortical areas. There is some evidence that this hierarchical organization may also be reflected in the spatial distribution of intrinsic timescales of activity. This ENIGMA working group intends to explore these patterns across the lifespan. To achieve the highest possible number of subjects, this needs to be done by meta-analysis.

Allison Nugent, PhD, ENIGMA MEG Chair
Jeff Stout, PhD, Lead Scientist
Anna Namyst, BA, Project Coordinator

MEG Working Group: Participating Institutions

Global Participation in the ENIGMA MEG Working Group
Global Participation in the ENIGMA MEG Working Group
  • Advent Health for Children
  • Arkansas Childrens Hospital
  • Aston University, UK
  • Cambridge University
  • Children's Hospital of Philadephia
  • DNISC (Università degli Studi G.D'Annunzio Chieti Pescara)
  • IRCCS San Camillo Hospital Venice
  • Johannes Gutenberg University, Mainz, Germany (Biomedical statistics and multimodal signal processing Unit)
  • Macquarie University
  • Massachusetts General Hospital
  • McGill University, Montreal Neurological Institute
  • National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
  • Nemours DuPont Hospital for Children
  • NeuroSpin
  • New York University and NYU Abu Dhabi
  • NIH/NICHD
  • NIH/NIMH
  • Precision Medicine Centre, Hokuto Hospital
  • Precision Medicine Centre, Kumagaya General Hospital
  • Salisbury VA Medical Center, Wake Forest University, Wake Forest School of Medecine
  • The Mind Research Network
  • Thomas Jefferson University
  • Universiti Sains Malaysia
  • Universiti Teknologi PETRONAS
  • University of Alabama, Birmingham
  • University of Göttingen
  • University of Jyväskylä, Finland
  • University of Pittsburgh
  • University of Pittsburgh
  • University of Texas Southwestern
  • University of Tübingen
If you are interested in participating in this project, please email the project coordinator, Anna Namyst, for more information.

Data Analysis

Data analysis will be available in two flavors: 1. Upload coregistered anonymized data to NIH 2. Perform analysis at acquisition site using EnigmaMeg scripts

Upload Data to be analyzed on NIH Biowulf cluster

Instructions for data preparation and upload: 

 ENIGMA MEG Data Upload

Potential MEG Subanalyses

 Healthy Volunteers
 Epilepsy
 Alzheimer's and dementia
 Motor Analysis
 Language Processing
 Anxiety Disorders
 Schizophrenia and related disorders
 Developmental disorders
 Traumatic Brain Injury
 Stroke
Retrieved from "https://megcore.nih.gov/index.php?title=ENIGMA_MEG_Working_Group&oldid=5585"