Dear Bruce, Steve, et al,
have you compared the output of mri_watershed with betsurf?
I ran a T1 volume through mri_watershed with the -surf output options. I also ran the same volume through betsurf. When comparing the two volumes, I specified an offset of -128 for the betsurf output. I expected a close correspondence between these surfaces. There is a slight rotation difference (see image attached).
Have you seen this before? Steve, is there some reason the betsurf output could be rotated?
Thanks, Darren