Re: [Freesurfer] Thalamic nuclei exited with ERRORS

[Yann Quidé]

External Email - Use Caution         Thanks for your help! I followed your instructions, but still have these issues. Actually, it seems to happen quite randomly, as I could process some subjects but not other, and also on subjects that I could previously process (I am using a loop for several subjects)! I attached logs from 1 subject for your information: for one the processing ran smoothly, for the others there are different errors…. This seems very odd; do you have any idea what is going on? Java1.8 is installed on my machine, and linked with Matlab (R2018b), but it seems that the MCR is running its own version, and not sure how to update the MCR version of Java… Thanks again for your help. Yann Note: the workaround from Matlab is to install some files from R2017b; my machine uses R2018b already, so not sure this is helpful.

log_segmentation_thalamus_fail1.log
Description: Binary data

log_segmentation_thalamus_fail2.log
Description: Binary data

log_segmentation_thalamus_success.log
Description: Binary data

On 30 Aug 2022, at 12:02 pm, fsbuild <fsbu...@contbay.com> wrote: MCRv84 looks like it should run on MacOS 10.13, so in a new terminal window, I would install it directly into the freesurfer distribution with, $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0 $ cd $FREESURFER_HOME $ rm -rf  MCRv84 $ cd bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b Then source the freesurfer setup script and try running things again to see if it works differently. The crash you listed looks like Matlab trying to run Java 1.7 which generates a segmentation fault.  There is a bug posting about this on The Mathworks web site, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://la.mathworks.com/matlabcentral/answers/697705-segmentation-violation-when-using-freesurfer-7-1-1-with-mcr-8-4   I do not have a login there to read the reply/workaround, but I do see postings that say a workaround is to run Matlab with the -nosplash flag at startup.. If you still get a crash with Java 1.7, you could try adding java 1.8 to your machine, switch to running 1.8, and see if it works differently.  There should be a Java icon in the system preferences panel on your machine which might help you manage java on your machine.  You can download Java 1.8 from the oracle web site under the MacOS entry on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.java.com/en/download/manual.jsp - R. On Aug 29, 2022, at 20:26, Yann Quidé <yannqu...@gmail.com> wrote:         External Email - Use Caution         Hi all, Just bumping this one up. Any help would be really appreciated. Thanks in advance, Yann On 27 Aug 2022, at 10:47 am, Yann Quidé <yannqu...@gmail.com> wrote: Hi team, I have been having troubles with processing my scans for thalamic subnuclei. In my previous post, I mentioned I was using FS7.3.2, but indeed realised that this version was not fully compatible with my OS (OSX 10.13). So I instead installed FS 7.2.0. However, I still have issues with the matlab runtime. I installed MCRv84, but received the  error  <crash report deleted > It seems that FS is looking for v84 files that are missing in v93? Does anyone have an idea of what I am doing wrong? Thanks in advance.. Yann On 20 Aug 2022, at 9:42 am, Yann Quidé <yannqu...@gmail.com> wrote: Not a good news for me, but thanks! Yann On 20 Aug 2022, at 06:40, fsbuild <fsbu...@contbay.com> wrote: 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 <yannqu...@gmail.com> wrote:         External Email - Use Caution         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 _______________________________________________ Freesurfer mailing list freesur...@nmr.mgh.harvard..edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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