Is it possible to get a T1w per sessions when using fMRIPrep?

In a longitudinal fMRI study with multiple T1w images per subject (one per session), I want to avoid averaging anatomical changes across time. By default, does fMRIPrep register all sessions to a single T1w template per subject (even without --longitudinal) — it seems so, correct?

Is there a way to ensure each session is aligned to its own session-specific T1w instead?

I’ve seen older posts on this, but wondering if there’s now a more sophisticated or supported way to achieve this.

Hi @konigsberg7, and welcome to neurostars!

The older advice you have likely seen is still probably correct. Using bids-filter-files and session-specific fs subject dirs is still the recommended way.

Best,
Steven