External Email - Use Caution Hello FreeSurfer developers,
I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). I am running FreeSurfer V.7.1.1 on my university’s high performance computing (HPC) system. I have Matlab R2014b installed in '/usr/local/freesurfer/MCRv84’). I greatly appreciate any suggestions on how to resolve this issue. Many thanks for your time and help. ------------------------------ USER mhua0773 HOST hpc008 PROCESSID 3344 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux pbsjob 6889001.pbsserver ------------------------------ freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 setenv SUBJECTS_DIR /scratch/Amy_FTD/controls_2_base/Preprocessing cd /scratch/RDS-FSC-Amy_FTD-RW/controls_2_base/Preprocessing /usr/local/freesurfer/7.1.1//bin/segmentHA_T1.sh 501_MRI1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Jun 13 13:59:28 AEST 2023 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64: failed to map segment from shared object: Operation not permitted Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile @#@FSTIME 2023:06:13:13:59:28 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 6.47 S 0.57 U 4.19 P 73% M 201140 F 0 R 61507 W 0 c 189 w 3872 I 0 O 84184 L 18.03 17.42 13.59 @#@FSLOADPOST 2023:06:13:13:59:34 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 18.03 17.43 13.61 Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Tue Jun 13 13:59:34 AEST 2023 Best regards, Mengjie
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