On 14 Jun 2023, at 2:56 am, freesurfer-request@nmr.mgh.harvard.edu wrote:

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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>

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       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-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

       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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