Hi Jess,
I agree with Jenni. It looks like it missed some of the white matter, which is why it also didn't get the pial surface. Was the wm.mgz accurate there? If it was, then the problem is probably the topology fixer. If not, then putting control points in the white matter would be my suggestion.
cheers, Bruce On Thu, 19 Apr 2007, Turner, Jessica wrote:
Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it?
Thanks,
Jess
Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324