External Email - Use Caution Hi FreeSurfer experts,
I am writing to follow up on the ‘invalidMEXFile’ error. I have tried to run the segmentation pipeline with both 7.1.1 and the dev version, but the problem persists. Unfortunately I don't have access to the Python version. Could you please provide any guidance on how to resolve the error? Many thanks for your time and help. Best regards, Mengjie > On 14 Jun 2023, at 2:56 am, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > > Message: 8 > Date: Tue, 13 Jun 2023 16:07:34 +0000 > From: "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error running hippocampus subfields and > amygdala nuclei segmentation pipeline > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <bl0pr04mb65315baa0800424c60740c87fd...@bl0pr04mb6531.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://secure-web.cisco.com/1F_Fn60gOLBwUunKZBm27pN6E84ujAaidUKXNEbDesv1Xm0k8zrO-5frHMP4mWIDdNqdZYXqGpyUCUUtD9v-DcbqDm-4zH9O6oud8cn4cfJwhh9YG4231328nnz_bcWh5q8QdzxbzTdfknp-ppXXPzbY9mQ0ft9M5rnr1SXNNTqbYM8IilXCPfTLKPpEqR3MjMxjHwpRhjDDr99p8GTNgaW9yWqfpERsDVYLpvmXCGn9oJB674n1EIlKSDQqs_1rG4ADw4ljr6UUEuoiSJ_VQm4ZYP7OXiPd7IJlVl7R6MZdHYwL0QoIdamc5QF45OrBr/https%3A%2F%2Fprotect-au.mimecast.com%2Fs%2Fx2GVCq71mwf19PRE5CMkfLN%3Fdomain%3Dmail.nmr.mgh.harvard.edu > > > ------------------------------ _______________________________________________ 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. 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