I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after intervention) and 1-month following the intervention.

I have been working with the recon-all longitudinal pipeline stream  (7.1.1) but have noticed pretty significant errors in terms of skull stripping and segmentation (participants are veterans with somewhat random lesion / atrophy patterns).

I have tested your new recon-all-clinical program (7.4.0) on some of my worst cases and it is performing remarkably well. I am doing some more digging into the various synth segmentation packages available in FS newest versions and was wondering what the best course of action would be for integrating recon-all-clinical or synthseg into a longitudinal workflow.

1.Could I use the recon-all-clinical outputs as the "cross" for later base and long template construction?

2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would it be feasible to use the independent segmentation extractions from those and bypass the longitudinal stream entirely (not saying I would want to but I am curious)?

Any and all help here would be greatly appreciated, and I thank you very much for your time.

Warmest regards,