fMRIPrep: how to reuse longitudinal AND pre-run FreeSurfer

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I’m unclear too. I think, for this case to work, you’ll need to also play with the new --fs-subjects-dir argument, so that a whole new FreeSurfer processing is done per session. Otherwise, I bet having a unique FS run will lead to ignoring sessions that were processed after the first.
How do you run FreeSurfer in your case? If you can’t run FreeSurfer independently per session, then you’ll need to:

  1. Run FS on your own
  2. Manipulate the FS outputs so that you have a different FS subject directory for each of >the sessions.

This is the exact workflow I figured out and implemented a few weeks ago, nice to have it confirmed! It seems to be working (I think…) except that I’m really unclear whether it’s indeed picking up the pre-run Freesurfer directory, see Detection of fs-subjects-dir in 20.0.2.

I’m currently running a few subjects with the working directory saved so I can get to the bottom of this (which I didn’t do the first time around).

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