Hi,
You are correct. mri_gcut is automatically done in v5.0 and not v5.1. If you want to run it using v5.1 you'll have to specify -gcut after -skullstrip. You can also try using a more conservative watershed threshold value to get rid of the extra dura if there's a lot of it.
-Khoa
On Thu, 3 Nov 2011, Vy Dinh wrote:
Dear Experts,
I've read that the latest Freesurfer release, v5.1, allows one to rerun the skullstripping step to remove extra dura. This would be a godsend for us since most pial surface corrections involve removing the dura. However, we have been using v5.0, which does not have this feature. It also appears that mri_gcut, the v5.0 equivalent of -gcut, is run by default in v5.0. Could someone please confirm this? I'd really appreciate it if there is a way to remove the extra dura automatically after running recon-all. Since we preprocessed our subjects using v5.0, we have not used v5.1 at all, unless it is more beneficial to start editing using v5.1.
Thanks in advance,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu