Difference between revisions of "MEG Software and Analysis"

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===== MEG Data Analysis =====
==== MEG Data Analysis ====


This section covers all aspects of MEG data analysis.
This section covers all aspects of MEG data analysis. The following pages assume that you have [[afni.nimh.nih.gov|AFNI]] installed and have a reasonably good idea of how to use it.


* [[CTF Tools|The CTF Tools in a Singularity Container]]
* [[DataTaskUtilities|Dataset and Task Utilities]]


* [[Pyctf|Accessing CTF Datasets from Python]]
* [[HeadLocMRICoreg|Head Localization and MRI Co-Registration]]


* [[Time Frequency Analysis|Time Frequency Analysis Tools]]
* [[SourceLocSAM|Source Localization - the SAM pipeline]]


===== Head Localization and MRI Co-Registration =====
* [[Head Localization and MRI Coregistration|Head Localization and MRI Co-Registration]]


* [[Source Localization - SAM|Source Localization - the SAM pipeline]]
The first step in any analysis pipeline is to localize the MEG data to anatomical space, which is generally done using a structural MRI. When doing this localization, it is important to know if the subject moved during the recording.


* [[Fun Stuff - How to make a movie| Fun Stuff - How to make a movie ]]
* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)


* [[MEG analysis on Biowulf| MEG analysis on Biowulf]]
{| class=wikitable width=600 align=center
|headMotionDetect -th 0.25 dataset.ds
|}


* [[Mne bids pipeline | MNE Bids Pipeline and BIDS background]]


* [[External MEG Analysis Toolboxes | Other Software packages]]
===== Dataset Utilities =====


* Converting Brainsight Localizers or AFNI fiducials [https://github.com/nih-megcore/nih_to_mne to tags or MNE transforms]
* Use parsemarks to

* Connectivity Analysis [[Connectivity Resources | Resources]]

* ICA Cleaning/Analysis [[ICA cleaning | ICA]]

* Github MEG Code for NIH Labs doing MEG research [[NIH Labs Github Pages | Github Links]]

==== Basic Tutorials for New/Inexperienced Researchers====

Most MEG Core scripts are written in bash, which is the command line interface to Linux. Python is a more powerful programming language, and Tom and Jeff have written some of our scripts in Python, but you don't really need to know how they work, just what they do. The AFNI tutorial below is geared towards fMRI/BOLD analysis. For MEG analysis you can ignore all the BOLD things, we just use it for statistics and display of the final source reconstruction results. If you want to go more in depth, Tom can explain the ones we use. Biowulf can be employed later when you want it all to go faster.

* HPC: Introduction to Linux -- https://hpc.nih.gov/training/handouts/Introduction_to_Linux.pdf
* HPC: Bash Class -- https://hpc.nih.gov/training/bash_class/
* Python Tutorial -- https://docs.python.org/3/tutorial/
* AFNI Introduction -- https://andysbrainbook.readthedocs.io/en/latest/AFNI/AFNI_Short_Course/AFNI_fMRI_Intro.html
* HPC: Introduction to Biowulf -- https://hpc.nih.gov/training/intro_biowulf


==== Stimulus Presentation Software ====

'''PsychoPy: Psychology software in Python'''
[http://www.psychopy.org PsychoPy] is an open-source application that allows you to run a wide range of neuroscience, psychology and psychophysics experiments. It’s a free, powerful alternative to Presentation™ or to e-Prime™, written in Python (a free alternative to Matlab™ ).
*[[Image:pdf.png]] [[Media:PsychoPyManual.pdf| Pyschopy documentation for release 1.90.2]]

'''Presentation: NeuroBehavioral Systems (NBS), Inc.'''
Presentation® is a stimulus delivery and experiment control program for neuroscience written for Microsoft Windows.
* [https://www.neurobs.com/presentation/docs/index_html Presentation online documentation]

'''E-prime 3: Psychology Software Tools'''
E-Prime® 3.0 software for behavioral research. ''Build your own experiments using E-Prime’s easy-to-use graphical interface. Design, collect, and analyze data – all within a few hours!''
* [https://pstnet.com/products/e-prime/ E-Prime 3.0 website]

====Miscellaneous Documentation====

* [[Image:adobe-ps.png]] [[Media:SensLayout-275.ps|SensLayout-275]] — a color picture showing the sensor names and relative locations (ps).
* [[Image:pdf.png]] [[Media:SensLayout-275.pdf|SensLayout-275]] - a color picture showing the sensor names and relative locations (pdf).
* [[Image:pdf.png]] [[Media:FileFormats.pdf|File Formats]] - CTF MEG data file format

Latest revision as of 12:20, 25 October 2022

MEG Data Analysis

This section covers all aspects of MEG data analysis. The following pages assume that you have AFNI installed and have a reasonably good idea of how to use it.

  • ICA Cleaning/Analysis ICA

Basic Tutorials for New/Inexperienced Researchers

Most MEG Core scripts are written in bash, which is the command line interface to Linux. Python is a more powerful programming language, and Tom and Jeff have written some of our scripts in Python, but you don't really need to know how they work, just what they do. The AFNI tutorial below is geared towards fMRI/BOLD analysis. For MEG analysis you can ignore all the BOLD things, we just use it for statistics and display of the final source reconstruction results. If you want to go more in depth, Tom can explain the ones we use. Biowulf can be employed later when you want it all to go faster.


Stimulus Presentation Software

PsychoPy: Psychology software in Python PsychoPy is an open-source application that allows you to run a wide range of neuroscience, psychology and psychophysics experiments. It’s a free, powerful alternative to Presentation™ or to e-Prime™, written in Python (a free alternative to Matlab™ ).

Presentation: NeuroBehavioral Systems (NBS), Inc. Presentation® is a stimulus delivery and experiment control program for neuroscience written for Microsoft Windows.

E-prime 3: Psychology Software Tools E-Prime® 3.0 software for behavioral research. Build your own experiments using E-Prime’s easy-to-use graphical interface. Design, collect, and analyze data – all within a few hours!

Miscellaneous Documentation

  • Adobe-ps.png SensLayout-275 — a color picture showing the sensor names and relative locations (ps).
  • Pdf.png SensLayout-275 - a color picture showing the sensor names and relative locations (pdf).
  • Pdf.png File Formats - CTF MEG data file format