I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010
make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1
The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was "recon-all -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", and saw the same error.
It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz)
The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Any ideas? Chris
you will need to get a fixed version of mri_ca_label from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
n.
On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote:
I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010
make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1
The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was "recon-all -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", and saw the same error.
It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz)
The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Any ideas? Chris _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, that did the trick. Chris
Nick Schmansky wrote:
you will need to get a fixed version of mri_ca_label from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
n.
On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote:
I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010
make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1
The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was "recon-all -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", and saw the same error.
It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz)
The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Any ideas? Chris _______________________________________________ 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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Chris Watson -
Nick Schmansky -
Watson, Christopher