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Cam_CAN_MEG_Resting_State_Pipeline

Welcome to the tvb-ccmeg wiki!

This repository contains a pipeline to clean and create source localized data for the resting state Cam-CAN MEG dataset. This pipeline was created by Dr. Simon Dobri and developed by Dr. Simon Dobri and Dr. Jack Solomon.

Repository Outline

This repository contains code that:

• Uses freesurfer to create parcellated structural MRI data
• extracts window of resting state data and cleans it using a bandpass and notch filter as well as either SSP or ICA motion correction.
• Projects data from sensor to source space using either a volumetric
  • Optionally parcellates the source level data

Dependencies

The dependencies for this analysis are as follows. (For in lab instructions please go to Running on Digital Research Alliance of Canada Infrastructure)

• mne (latest)
  • If using the cedar preinstalled mne wheel the additional dependencies are:
    • nibabel (latest)
    • sklearn (latest)
    • python-picard (latest)

The scripts were run in python 3.11.4 for publication. They may work with other versions of python but are not guaranteed to function correctly.

For users from McIntosh Lab or those with DRA allocations, please refer here: Running on Digital Research Alliance of Canada Infrastructure
For other users, please refer here: Running on General Linux Systems