Apologies for bumping an old conversation, but I’m interested in whether you ever sussed out the precise difference here between Freesurfer’s longitudinal pipeline and fmriprep’s averaging approach?
It also seems to me, correct if I’m wrong, that what @atersakyan originally wanted could be implemented now in 20.0.1! Using the new bids-filter-file flag and filtering out session =1 vs session = 2, etc. I am working under this assumption and was trying to figure out what a .json file to do that would look like, and how to point fMRIprep to the correct cross-sectionally-run Freesurfer directory for a subject.
Though I’m unclear how filtering inputs with the bids-filter-file interacts with what is written to derivatives/freesurfer, it seems like this could be done.