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…

Short answer: no, that would not be possible ATM.

If you don’t want to make any cross-session reference of the BOLD data, then the easiest workaround is to unfold your subjects into two (i.e., instead of having two sessions under one subject, have two single-session subjects).