I got a little ahead of myself and ran first on brain-extracted 60 subjects (with the -b flag) before noticing in the documentation that this was "generally discouraged". The subcortical registrations look fine for the most part, and the segmentation looks accurate. Why is using brain-extracted data discouraged?
BTW, this program is wonderful. It's great to see FIRST segment these T1's so quickly and accurately, especially to someone who used to hand segment T1's in the same way (CMA).
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