Pre-run, multi-session FreeSurfer and fMRIPrep


Regarding using pre-run freesurfer outputs. I have succesfully done so when each ‘sub’ has only 1 session. However, I am trying to place Freesurfer outputs for session two now (in /fmriprep/out/freesurfer), but since the folders there are organized by ‘sub’ level I can’t place another folder for session two with the same name. How should I include 2 timepoints/sessions of pre-run Freesurfer data? Can the Freesurfer ‘sub’ folders also contain ‘ses’ subfolders?


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4 posts were merged into an existing topic: Multiple scan sessions some bad anatomicals