Hi,
Atm, I (1) use fprep to get the prreprocessed bold in the native space for each run and session (2) realign these to a single reference (the fprep ref image from the first run and session).
The second step is not ideal but works ok for now.
Apparently, sbref option can be used, but it is a bit more work and I haven’t tried it yet. See [this] post(fMRIPrep coregistration within sessions?).
Hope that helps