Hi Julia, I have a dataset in need of the same functionality as you. Mine has a baseline session and a session after 1 year, and I expect there to be some changes in the T1s over the course of the year.
For now, similar to @Steven’s comment, I have been using a bids-filter json file to specify the session I want (eg. baseline), which I include in my fmriprep command with the flag --bids-filter-file. I then run fmriprep separately for my two sessions (if you have more, you would need to run it once for every session) and have each write to a different output directory to avoid overwriting of any directories or files with non-unique names. Lastly, I run a script to merge my two output directories into a single output directory in bids format. I know it’s a little annoying to do it this way, but it works.
I hope this helps!
-Debbie
PS (@effigies): Perhaps in the future fmriprep could have an option for this kind of longitudinal processing to avoid having to merge output directories at the end. I would really appreciate this!