fMRIPrep: how to reuse longitudinal AND pre-run FreeSurfer

[oesteban]

@Ursula_Tooley

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.

This seems like the most straightforward approach, although I admit it entails quite a lot of boilerplate (and also has the culprit you already picked up - comment below).

@Ursula_Tooley

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.

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.

Does this make sense to you?