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
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 ?
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.