-
Notifications
You must be signed in to change notification settings - Fork 0
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****
To create the group summary stats for cortical and subcortical volumes
Change the current working directory to the freesurfer directory:
cd /Volumes/psybrain/R33/freesurfer/freesurfer
Export the subjects dir:
export SUBJECTS_DIR=/Volumes/psybrain/R33/freesurfer/freesurfer/
Run freesurfer commands:
/Applications/freesurfer/bin/asegstats2table --subjectsfile subjectlist.txt --tablefile R33_asegstats2table.txt
/Applications/freesurfer/bin/aparcstats2table --subjectsfile subjectlist.txt --hemi rh --tablefile R33_aparcstats2table_righthemi.txt
/Applications/freesurfer/bin/aparcstats2table --subjectsfile subjectlist.txt --hemi lh --tablefile R33_aparcstats2table_lefthemi.txt