Fmri prep for multi site T1 preprocessing

[Pradeepa_Ruwan]

Dear Experts,

We have been organizing multi-site data in BIDS, collecting longitudinal data across six sessions from three sites (multi-vendors). As we are about to run fMRIprep, we realize it is tricky to get T1 preprocessing for each session. I have seen this old thread about this issue:

Fmriprep- run the anatomical workflow individually on each session, without merging/averaging

I have a dataset where subjects came in for 2 sessions, now when I run fmriprep I noticed that the T1 images from all sessions are merged under a single “anat” folder in fmriprep/$subj/anat while all the functional data that are processed are under their individual session folders. Is there anyway for me to do that for anatomical as well, so that each session’s anatomical data under derivatives/fmriprep is under it’s own session?- Rather than creating a “new subject” for each session…

Are there any new updates since then? How can we achieve T1 preprocessing for each session without restructuring the MRI data?

Thank you.

Best regards,
Ruwan

[Steven]

Hi @Pradeepa_Ruwan,

You can use BIDS filter files and specify a different FS subjects directory for each session.

Best,
Steven