My lab runs our own FreeSurfer (6 and 7) pipeline for most data we work with. I’d like to not re-create that data with FmriPrep. I’ve read this link about the option --fs-subjects-dir
.
It’s unclear how to use this option. We make the FS sub directory named after the T1 series code not the subject. There’s too many alternative anatomical scans we treat them all separately.
Can I still use my FS outputs ? What paths need to exist and where ?
Thank you
UPDATE:
I made a copy of my FS outputs and placed in a new directory not in the bidsdir
and added what I think is the expected sub-DPOP006
directory name to hold them. Of course I had to add a binding for the singularity container.
I tried using a sym link but that failed the validator. Perhaps this will work if I skip validation.