Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being killed even tough I added -debug. The cluster is running sbatch and CentOS release 6.4. Are there any debug options I can add or are there any debugversion of mri_ca_register I can download? This happen every time I run the program. I have asked for 8g ram when ran the program.
Best regards Knut Jørgen Bjuland
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send the rest of the log. Knut J
#-------------------------------------- #@# CA Reg Thu Sep 12 19:59:01 CEST 2013 /cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a ll_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log
======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.55 (predicted orig area = 5.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.932, neg=0, invalid=96777
On 09/12/2013 10:14 AM, Knut J Bjuland wrote:
Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being killed even tough I added -debug. The cluster is running sbatch and CentOS release 6.4. Are there any debug options I can add or are there any debugversion of mri_ca_register I can download? This happen every time I run the program. I have asked for 8g ram when ran the program.
Best regards Knut Jørgen Bjuland
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Closed, not bug in Freesurfer.
On 09/12/2013 10:31 PM, Knut J Bjuland wrote:
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send the rest of the log. Knut J
#-------------------------------------- #@# CA Reg Thu Sep 12 19:59:01 CEST 2013 /cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a ll_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log
======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.55 (predicted orig area = 5.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.932, neg=0, invalid=96777
On 09/12/2013 10:14 AM, Knut J Bjuland wrote:
Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being killed even tough I added -debug. The cluster is running sbatch and CentOS release 6.4. Are there any debug options I can add or are there any debugversion of mri_ca_register I can download? This happen every time I run the program. I have asked for 8g ram when ran the program.
Best regards Knut Jørgen Bjuland
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Knut J Bjuland