Check your log. If gcut detects that the gcutted brain is much smaller than the original brain, it will assume that something bad has happened and it won't write brainmask.gcuts.mgz. This may be what is happening in your case. To fix this, you can adjust the watershed threshold or add something like 'mri_gcut -T 0.3' to your expert options file. The lower the threshold passed to mri_gcut -T, the less likely gcut will be to remove too much brain.
On Tuesday, October 23, 2012 14:28:19 Vincent wrote:
I'm attempting to remove some dura which is affecting my surfaces, but upon completion of running gcut I can see no differences in my images, nor can I use tkmedit to view my T1 with brainmask.gcuts.mgz, because it says it "couldn't import the segmentation volume". I looked for brainmask.gcuts.mgz but using ls recursively and grepping for it, but I can't find it anywhere. What explanations might there be for this? Thank you in advance.
::vincent