the holes that are interior and don't have any surface adjacent to them are fine. The others you may need to edit the wm.mgz, but it's impossible for us to tell from just this image. Make sure you look at the data in multiple orientations to see whether those voxels should have been labeled wm or not.
cheers Bruce
On Fri, 16 Nov 2012, Catherine Bois wrote:
Hi,
I have a question re the screenshot attached in the present email... Several slices of the white matter mask of this scan seem to have several " holes" ie black spots like this. These parts are included in the brain mask, but the brain mask seems to be quite non-uniform in terms of "whiteness" of the brain mask. I have gone in and filled some in manually; ie done white matter edits, is this the correct way to fix this problem, or do the holes indicate some other problem?
Thank you very much for your help,
Regards Cathy