The version is freesurfer-Linux-rh9-stable-pub-v3.0.2. The error message happens when I try to run recon-all -s <subj> -segmentation, which fails to locate the brain.mgz file (the brainmask.mgz is there instead).
Besides this, I can't run tksurfer because an error message appears saying:
mrisReadTriangleFile(~/freesurfer/subjects/bert/surf/rh.sphere.reg): surface doesn't match ~/freesurfer/subjects/bert/surf/rh.smoothwm
mrisReadTriangleFile failed
Then I only have a transparent window...
Thanks again!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Jenni Pacheco Sent: 28 April 2006 12:14 To: 'Joao Pereira'; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Skullstripping
Which version of Freesurfer are you using? The newest versions write a file called brainmask.mgz, but the subsequent steps do recognize and use this. Can you elaborate more on the specific problems/error messages you are encountering?
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Joao Pereira Sent: Friday, April 28, 2006 6:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstripping
Can someone explain me why my the recon-all skull stripping option is writting a file named brainmask.mgz instead of brain.mgz? This is a problem because the subsequent procedures do not recognize the file.
Thank you!
JP
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