Sender: LSF System Subject: Job 9168895: in cluster Exited Job was submitted from host by user in cluster at Fri May 1 12:21:05 2020 Job was executed on host(s) <4*lc04a23>, in queue , as user in cluster at Fri May 1 12:21:07 2020 was used as the home directory. was used as the working directory. Started at Fri May 1 12:21:07 2020 Terminated at Fri May 1 12:21:29 2020 Results reported at Fri May 1 12:21:29 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #!/bin/bash #BSUB -J Hippo1_003_S_4288 # Job name #BSUB -P acc_zhangb03a # allocation account or Unix group #BSUB -q premium # queue #BSUB -n 4 # number of compute cores #BSUB -W 00:30 # walltime in HH:MM #BSUB -R span[ptile=4] #BSUB -R rusage[mem=4000] # 4 GB of memory requested #BSUB -o %J.stdout # output log (%J : JobID) #BSUB -eo %J.stderr # error log #BSUB -L /bin/bash # Initialize the execution environment module load freesurfer/7.0.0 module load matlab_runtime/R2014b export FREESURFER_HOME=/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer export SUBJECTS_DIR=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288 cd $SUBJECTS_DIR segmentHA_T1_long.sh 003_S_4288_base ------------------------------------------------------------ Exited with exit code 1. Resource usage summary: CPU time : 19.00 sec. Max Memory : 666 MB Average Memory : 282.00 MB Total Requested Memory : 16000.00 MB Delta Memory : 15334.00 MB Max Swap : - Max Processes : 12 Max Threads : 37 Run time : 22 sec. Turnaround time : 24 sec. The output (if any) follows: #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) left Fri May 1 12:21:10 EDT 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/lib64:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//runtime/glnxa64:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//bin/glnxa64:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//sys/os/glnxa64:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/sys/java/jre/glnxa64/jre/lib/amd64:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/sys/java/jre/glnxa64/jre/lib/amd64/server:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/sys/os/glnxa64:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/bin/glnxa64:/hpc/packages/minerva-common/Mathworks/matlab/R2014b_runtime/v84/runtime/glnxa64:/hpc/lsf/10.1/linux3.10-glibc2.17-x86_64/lib Registering imageDump.mgz to hippocampal mask from ASEG of Base Point 7.0.0 --mov: Using imageDump.mgz as movable/source volume. --dst: Using /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped_opened.mgz as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... -------------------------------------------------------------------------- ERROR: FreeSurfer license file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/bin//mri_robust_register --mov imageDump.mgz --dst /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped_opened.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Signal 127 cp: cannot stat 'imageDump_coregistered.mgz': No such file or directory mv: cannot stat 'imageDump_coregistered.mgz': No such file or directory 7.0.0 --mov: Using imageDump.mgz as movable/source volume. --dst: Using /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped_opened.mgz as target volume. --lta: Output transform as rigidToAffineBase.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --affine: Enabling affine transform! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... -------------------------------------------------------------------------- ERROR: FreeSurfer license file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/bin//mri_robust_register --mov imageDump.mgz --dst /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped_opened.mgz -lta rigidToAffineBase.lta --mapmovhdr imageDump_coregistered.mgz --affine --sat 50: Signal 127 mv: cannot stat 'imageDump_coregistered.mgz': No such file or directory Registering hippocampal masks of time points to mask of base 7.0.0 --mov: Using hippoAmygBinaryMask_tp_1_autoCropped.mgz as movable/source volume. --dst: Using /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume. --lta: Output transform as tp_1_to_base.lta . --mapmovhdr: Will save header adjusted movable as kk2.mgz ! --affine: Enabling affine transform! --sat: Using saturation 50 in M-estimator! reading source 'hippoAmygBinaryMask_tp_1_autoCropped.mgz'... -------------------------------------------------------------------------- ERROR: FreeSurfer license file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/bin//mri_robust_register --mov hippoAmygBinaryMask_tp_1_autoCropped.mgz --dst /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped.mgz -lta tp_1_to_base.lta --mapmovhdr kk2.mgz --affine --sat 50: Signal 127 7.0.0 --mov: Using hippoAmygBinaryMask_tp_2_autoCropped.mgz as movable/source volume. --dst: Using /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume. --lta: Output transform as tp_2_to_base.lta . --mapmovhdr: Will save header adjusted movable as kk2.mgz ! --affine: Enabling affine transform! --sat: Using saturation 50 in M-estimator! reading source 'hippoAmygBinaryMask_tp_2_autoCropped.mgz'... -------------------------------------------------------------------------- ERROR: FreeSurfer license file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/bin//mri_robust_register --mov hippoAmygBinaryMask_tp_2_autoCropped.mgz --dst /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left//hippoAmygBinaryMask_autoCropped.mgz -lta tp_2_to_base.lta --mapmovhdr kk2.mgz --affine --sat 50: Signal 127 rm: cannot remove 'refTP*.lta': No such file or directory Reading contexts of file /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt Constructing image-to-world transform from header information (asegModCHA_tp_0.mgz) Constructing image-to-world transform from header information (/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/tmp/hippoSF_T1_long.v21_left/imageDump.mgz) Error using kvlGEMSMatlab /usr/pubsw/packages/itk/4.9.1/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: itk::ERROR: Region ImageRegion (0x2ac303ffb070) Dimension: 3 Index: [309, 634, 0] Size: [18446744073709551563, 18446744073709551238, 2] is outside of buffered region ImageRegion (0x2ac2f2693c88) Dimension: 3 Index: [0, 0, 0] Size: [256, 256, 256] Error in kvlReadCroppedImage (line 11) Error in SegmentSubfieldsT1Longitudinal (line 403) @#@FSTIME 2020:05:01:12:21:10 run_SegmentSubfieldsT1Longitudinal.sh N 16 e 18.49 S 2.77 U 9.69 P 67% M 910956 F 369 R 334255 W 0 c 1551 w 11253 I 757072 O 0 L 13.79 15.65 15.47 @#@FSLOADPOST 2020:05:01:12:21:29 run_SegmentSubfieldsT1Longitudinal.sh N 16 13.98 15.58 15.45 Linux lc04a23 3.10.0-957.el7.x86_64 #1 SMP Thu Nov 8 23:39:32 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux longitudinal subfields exited with ERRORS at Fri May 1 12:21:29 EDT 2020 For more details, see the log file /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/003_S_4288_base/scripts/long-hippocampal-subfields-T1.log PS: Read file <9168895.stderr> for stderr output of this job.