hmmmm, if the euler number is correct (2) then there can't be any holes, as it is a topological invariant. Are you sure the euler number is the same for all your surfaces (i.e. orig, white, pial, inflated, sphere, sphere.reg)? Are you using mris_euler_number to compute it?
cheers, Bruce
On Fri, 3 Sep 2004, Goldman, Aaron (NIH/NIMH) wrote:
Hi, I'm trying to do surface-based cross-subject analysis on a quite large group of participants, but I've been having unexpected problems with holes remaining on the finished surface. They aren't detected with euler's number, but they create problem areas when I try to convert the surfaces to a standard mesh using another program (SUMA), and produce visible distortions on the sphere.reg. When I go back to freesurfer, I can find the holes by opening the sphere and zooming in on the problem area, and as far as I can tell it usually turns out to be a single voxel causing the problem, rather than a large area that should have been manually edited. Is there any automated way to correct these defects with freesurfer, since trying to manually fix them would be extremely inefficient? Thanks.
-Aaron-
PS - I have some jpeg examples I can send if it would be helpful, but didn't attach them because of the list's limitation on email size.
Aaron L. Goldman
Post-Bacc IRTA
Genes, Cognition and Psychosis Program, NIMH
Building 10, Room 3C108
Phone: (301) 435-0944
Email: mailto:aarong@mail.nih.gov aarong@mail.nih.gov