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" <malshi...@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 !! Mohamad _______________________________________________ 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
