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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there a reason you are just running -segmentation? If you are running everything by the individual steps (and not using the -autorecon flags) it is possible you have missed some of the steps. If you've skipped some steps this is likely causing the problem, specifically, if you've skipped -normalization2.
Jenni
On Fri, 28 Apr 2006, Joao Pereira wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Joao,
The message about 'surface doesnt match' indicates an incomplete run (rh.sphere.reg should be newer than rh.smoothwm). It will be necessary re-run autorecon2 and autorecon3 on the rh. This wiki page is very handy for tracking problems with step-by-step runs:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Nick
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Jenni Pacheco -
Joao Pereira -
Nick Schmansky