Hi Dylan,
Thanks very much for the update - that seems like a great plan to me.
Regarding the --logitudinal flag - it only determines how FreeSurfer is going to calculate the T1w average. So you need to split it by sessions. If all sessions have one T1w, then you’d be fine. If you want/may group sessions (e.g. you have a test-restest protocol run on September for 5 years – 10 sessions that go in pairs), then more tricky settings will be necessary.
More on that here: fMRIPrep: how to reuse longitudinal AND pre-run FreeSurfer
Finally, I’d like to bring one discussion @satra usually takes care of clarifying. FreeSurfer via fMRIPrep is not exactly FreeSurfer and should be considered as a variant. In other words: you either run FreeSurfer on its own or via fMRIPrep. But don’t mix both.