hmmm, that's interesting. If you send us the data we'll take a look. In any case, you can run, if you create an orig_stripped.mgz you can run:
mri_mask T1.mgz orig_stripped.mgz brain.mgz
then you should be able to run from after the skull stripping forward (check the recon-all help. You'll need to run a couple of steps before autorecon2-wm and autorecon3).
cheers Bruce
On Fri, 8 Aug 2008, Vina Goghari wrote:
Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty !
I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process?
Thanks, Vina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer