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Hello Yann,

It looks like the system library, /usr/lib/libSystem.B.dylib, is too old on your machine running MacOS (10.13) to work with the Matlab MCRv97 runtime environment.   MacOS 10.13 (High Sierra), 10.14 (Mojave) - are no longer supported by Apple.  Soon Apple will also drop support for MacOS10.15 (Catalina).  I think you would need to upgrade to Catalina to use the Matlab R2019b release as installed by the script ./freesurfer/bin/fs_install_mcr

- R.

On Aug 19, 2022, at 07:33, Yann Quidé <yannquide@gmail.com> wrote:

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Hi team,

I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13).
However, I receive the below error.
Any idea how I could solve this?

Thanks in advance.

Yann

------------------------------
USER yann
HOST Ians-Mac-Pro.local
PROCESSID 86082 
PROCESSOR x86_64
OS Darwin
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
------------------------------
freesurfer-darwin-macOS-7.3.2-20220804-6354275
 
setenv SUBJECTS_DIR /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/Subjects
cd /Volumes/MacintoshHD2/mridata/IGP/ENIGMA_SZ_Thalamic_nuclei/ENIGMA_BARI
/Applications/freesurfer/7.3.2/bin/segmentThalamicNuclei.sh sub-BA_IGP001

#--------------------------------------------
#@# Thalamic Nuclei processing Fri 19 Aug 2022 20:10:24 AEST
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.3.2/MCRv97//runtime/maci64:/Applications/freesurfer/7.3.2/MCRv97//bin/maci64:/Applications/freesurfer/7.3.2/MCRv97//sys/os/maci64:/Applications/freesurfer/7.3.2/lib/gcc/lib:
Invalid MEX-file '/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64': dlopen(/private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: ____chkstk_darwin
  Referenced from: /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib
 in /private/tmp/MCR_3324153754/.mcrCache9.7/Segmen0/Users/developer/eugenio/GEMS2.build/bin/kvlGEMSMatlab.mexmaci64

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 139)

MATLAB:mex:ErrInvalidMEXFile
Darwin Ians-Mac-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64

Thalamic nuclei exited with ERRORS at Fri 19 Aug 2022 20:11:24 AEST






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