Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Nathan,
Can you send me the recon-all.log file for that subject? Its found in the <subjid>/scripts dir.
Nick
On Fri, 2009-02-13 at 15:15 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what files are in [subject path]/mri/*aseg*.mgz?
On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz. The scans that are working seem to have aseg.auto_noCCseg.mgz instead of CCseg.mgz.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 2/13/2009 8:44 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] still exiting with errors
what files are in [subject path]/mri/*aseg*.mgz?
On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the current versions should have aseg.auto_noCCseg.mgz. When you rerun recon-all doesn't it create them?
On Sun, 15 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz. The
scans that are working seem to have aseg.auto_noCCseg.mgz instead of CCseg.mgz.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 2/13/2009 8:44 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] still exiting with errors
what files are in [subject path]/mri/*aseg*.mgz?
On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No. At least for this particular subject, when I run recon-all it does not create the noCCseg file. However, I have only been starting from autorecon2. Does this make a difference? Also, I have just downloaded version 4.2...if I run it using the new version will it create the files I need? Also, I have a subject who outputs this error:
mris_make_surfaces: could not read segmentation volume /misc/data14/jen/FreesurferTest/JPP_111/surface_2/mri/aseg.mgz
This subject DOES have the noCCseg file. I've sent the recon-all.log files to Nick Schmansky, maybe that will shed some light on the issue.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 2/16/2009 3:33 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] still exiting with errors
the current versions should have aseg.auto_noCCseg.mgz. When you rerun recon-all doesn't it create them?
On Sun, 15 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz. The
scans that are working seem to have aseg.auto_noCCseg.mgz instead of CCseg.mgz.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 2/13/2009 8:44 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] still exiting with errors
what files are in [subject path]/mri/*aseg*.mgz?
On Fri, 13 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
and
ERROR: cannot find [subject path]/mri/aseg.mgz
Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Dankner, Nathan (NIH/NIMH) [F] -
Nick Schmansky