FreeSurfer Analyses

Free Surfer Analyses are carried out using FMRIprep: https://fmriprep.readthedocs.io/en/stable/

export FS_LICENSE=/Users/memlab/license.txt fmriprep-docker /Volumes/psybrain/R33/BIDS \ /Volumes/psybrain/R33/freesurfer \ participant -w /Volumes/psybrain/R33/fsworkdir \ --notrack --ignore slicetiming -v --skip_bids_validation --mem_mb 8000 --anat-only --output-spaces fsaverage5 --anat-only \ --participant_label 1****

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To create the group summary stats for cortical and subcortical volumes

cd to freesuerfer directory:

cd /Volumes/psybrain/R33/freesurfer/freesurfer

export the subjects dir:

export SUBJECTS_DIR=/Volumes/psybrain/R33/freesurfer/freesurfer/

run free surfer command:

/Applications/freesurfer/bin/asegstats2table --subjectsfile subjectlist.txt --tablefile R33_asegstats2table.txt