FmriPrep: Using Existing FreeSurfer Run

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

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.

The fs-subjects-dir should go to a folder, in which each directory is named for one of your subjects. In that folder should be the recon-all outputs from FreeSurfer. If you don’t have the folders set up like this already, you can use symlinking ln -s source destination to create shortcuts in the style described above, and fmriprep should treat it correctly. You should make sure if you set up a symlink option that ALL relevant drives (that is, the source and destination) are available to your container, assuming you are using Docker/Singularity.

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Thanks Steven.

The FS subject directory copy worked as long as I added the new sub dir with the sub-XXXX.
So I guess sym links won’t work unless I bind the linked tree to the container.