External Email - Use Caution        

I’ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version?

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation

Cheers,

/E

 

--

Juan Eugenio Iglesias

http://www.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

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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.

 

 

------------------------------

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