Hi Mohamad, you might have run out of memory. Could you please try allocating more RAM for the job? Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Mohamad J. Alshikho" MALSHIKHO@mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 4, 2016 11:01:50 PM Subject: [Freesurfer] Brain stem segmentation-- FS6
Dear Freesurfer experts, I am working on brain stem segmentation analysis using the new module included in FS6.
The analysis ran properly for 38/40 subjects. I have an issue with two subjects.
I sent my jobs to the cluster as always using the following command line: pbsubmit -c " recon-all -subjid <SUBJECT ID> -brainstem-structures " -f <email address> &
After a while I received an email that the job is done: PBS Job Id: 11020983.launchpad.nmr.mgh.harvard.edu Job Name: pbsjob_2045 Exec host: compute-0-111/3 Execution terminated Exit_status=0 resources_used.cput=00:42:33 resources_used.mem=3220236kb resources_used.vmem=7319444kb resources_used.walltime=00:44:45
I checked the subject's folder /mri/ looking for the files : "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" but I was unable to find them.
I checked the job history in the cluster and it returns as ( quotation -- the last lines):
Resolution level 3 iteration 3 deformation iterations 19 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.0097272 voxels in 4.1676 seconds
minLogLikelihoodTimesPrior =
1.0786e+07
Resolution level 3 iteration 3 deformation iterations 20 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.016365 voxels in 4.1717 seconds
minLogLikelihoodTimesPrior =
1.0786e+07
Fitting mesh to image data mask took 2144.0218 seconds Error using kvlAtlas3D_Matlab std::bad_alloc
Error in kvlRasterizeAtlasMesh (line 11)
Error in segmentSubject (line 1078)
Started at Thu Feb 4 15:57:18 EST 2016 Ended at Thu Feb 4 16:41:59 EST 2016 #@#%# recon-all-run-time-hours 0.745 recon-all -s CTRL039 finished without error at Thu Feb 4 16:42:00 EST 2016
It stated that the job was ended properly without errors but the previous lines ( before the final stamp) showed errors and the files "brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" are missing ...
Kindly what I am doing wrong? Any suggestions are highly appreciated !!
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