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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-request@nmr.mgh.harvard.edu wrote:

Message: 8 Date: Tue, 13 Jun 2023 16:07:34 +0000 From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@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: BL0PR04MB65315BAA0800424C60740C87FD55A@BL0PR04MB6531.namprd04.prod.outlook.com

Content-Type: text/plain; charset="windows-1252"

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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_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzOE... Cheers, /E

-- Juan Eugenio Iglesias http://secure-web.cisco.com/1QfGfcEcTkVF9fEP1hlZPh1BIK3eVs0WEnf3b34X1Z7TR0_9...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mengjie Huang mhua0773@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

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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.

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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

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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