I've just been verifying by viewing the transformed tracts and FA maps together in DSI Studio. I'm currently applying some ROI masks to the tracts of a healthy control using Matlab to create a connectivity matrix, so if the resulting matrix seems really off then I'll reorient my original FA image.

I was going through the methods of the Mori lab paper that the Vista Lab cited in their AFQ_SegmentFiberGroups script, and it looks like they also registered each subject's T1-weighted volume to their template and applied that transformation to their tracts as well. Do you think that's worth doing in this case?