External Email - Use Caution I’ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version? https://secure-web.cisco.com/1Cv_49AxchVd_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzOEqT7zCC8a1jFBudPBWmbpay8jscwU4QvGJDaMi2Cexs8SJBYFvrJeX-LR2OR0B-B8vsfZAAwbH2I-SxMVz-0j11O6kyXk11-6yoQP-d4CnlFCsvirTUTv7SLsIpCFdmoyu22uygYL-Xeef5uWjZlOpVC5xvNwf0vRAG9N4jHJLWQvB4rIH8U1NczWHumTV-HX3kNsO44ykNapycKco7/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentation Cheers, /E
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1QfGfcEcTkVF9fEP1hlZPh1BIK3eVs0WEnf3b34X1Z7TR0_9pPG-9ruSX2PaS1LaTC-REt8YLrAGgk1eeDTYYfBiJzLTOEjVrGgCYTegQUu5qHJUk0ksw6psnh7nYUCtGbi4T6AbAtLguHTvmFHGRHUgBFd3Q7qQ00jpLSVu9RuIn1eIHOUZ46QGhRpawXIzi0vBMmmqbh8zasIVV5bOLjB2WfPcwXDBhVILH07Ir8CD7ZItyjBuPBJvHvsHKG6DV/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mengjie Huang <mhua0...@uni.sydney.edu.au> Date: Tuesday, June 13, 2023 at 8:12 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline 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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