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Thanks again for your help. I tried with both R2017b and R2019b but no luck. When I soft link either of these versions to MCRv84, I receive the following error:

sub-BA_IGP001 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Wed 31 Aug 2022 09:12:43 AEST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib: dyld: lazy symbol binding failed: Symbol not found: __Z14standaloneMainRKSt6vectorISsSaISsEEbb Referenced from: /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei Expected in: /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

dyld: Symbol not found: __Z14standaloneMainRKSt6vectorISsSaISsEEbb Referenced from: /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei Expected in: /Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwlaunchermain.dylib

/Applications/freesurfer/7.2.0/bin/run_SegmentThalamicNuclei.sh: line 33: 49189 Abort trap: 6 /Applications/freesurfer/7.2.0/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei sub-BA_IGP001 /Volumes/MacintoshHD2/mridata/IGP/Subjects 0.5 /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr /Applications/freesurfer/7.2.0/bin/' 1 0 134 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 Wed 31 Aug 2022 09:12:45 AEST

For more details, see the log file /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/scripts/thalamic-nuclei-mainFreeSurferT1.log

/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz .

If I use folders named MCRv93 or MCRv97, freesufer asks me to install R2014b…

Is there any other option?

Thanks in advance.

Yann

On 31 Aug 2022, at 6:24 am, fsbuild fsbuild@contbay.com wrote:

One error in the logs is from missing symbols in the Matlab java library, and another says to contact the Mathworks for technical support. But Mathworks is not going to support you because MacOS 10.13 does not meet the system requirements for R2014b.

You don’t have to upgrade to MacOS 10.14 or 10.15 to run R2019b per https://secure-web.cisco.com/1W8S3KSrnNfB7GaLAK6G1uuF5_rci5S4HvSmtU8OkqtOAlG... https://secure-web.cisco.com/1W8S3KSrnNfB7GaLAK6G1uuF5_rci5S4HvSmtU8OkqtOAlGdPsYx3jEm1z4Y7OmHeVtslmW-9uIZbPNIVgRvK0auH-mQsUSd_0q8QN4YPKjmGexCKIpvv-P0yefReTJqxWhMfLBcfcves8ir9RzBwOrSiaGI0pMlRnZScJYf35Jet-9xRV6-FDUduEe2WcQh8cceh3UsJbGSMj6Kk1ZHugtKo3wDqrpO221zNeVVcGR3ZP8q2pOJ63hj0ksourfzxewbP2QruVHmsWlvSZ5cEb1Tfi5YLscbi6lvf061m_DxCLSvTaqCt7WYONZLZ6CPkRIRjnA7-BlhaE9VqlcyRyg/https%3A%2F%2Fwww.mathworks.com%2Fcontent%2Fdam%2Fmathworks%2Fmathworks-dot-com%2Fsupport%2Fsysreq%2Ffiles%2Fsystem-requirements-release-2019b-macintosh.pdf

• but the oldest version of MacOS you can run with R2019b is *exactly* MacOS 10.13.6 and not an earlier version. You should be able to use the MacOS software update tool to update to 10.13.6 if you are not already running it. I recommend that as I believe that is the last/most stable version of MacOS 10.13. From the compatibility chart, https://secure-web.cisco.com/1kdVJWn7q7Z57Ogi3jAMS7tFUwuSagRqWDZlskobrq4cl1s... https://secure-web.cisco.com/1kdVJWn7q7Z57Ogi3jAMS7tFUwuSagRqWDZlskobrq4cl1sACpVxcYANzfMNcuiIFixCe6sTjnWTT5u-L1AMA58ggKROWRK96WyFtIROUwgw-NTWSirLB5iqdf4mioDJxrsLO1VwKBvnARc_6LDlILK0reXDfIlCnGXYfnVKdEo-wEFEbteimCojgdl2Xxp6JKb_WpB_F4kvLBsg-fwrN7VE0lj4qw-dXWJOuoAxJ1Mxnknqqn6OTpckOngEt-UV378H6N8xQ7uHnXK77Ldf7b7Bbuyx3Cuf2-fDyVoJuT5kzEO8ghurIRk-JIe-NiAojL-Yxp4Hr2PrGdEXg4CF8ag/https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Frequirements%2Fprevious-releases.html, it looks like you could also try the older R2017b release. I think you tried R2019b before with the freesurfer 7.3.2 release but not with the 7.2.0 release which you are now running.

You can follow the same instructions below to install R2019b or R2017b with the fs_install_mcr script and see if you get different results. You should only have one ./freesurfer/MCR* subdir present at any one time. It’s not clear to me the java libraries included in the Mathworks runtime environment care about the version of Java installed in MacOS, e.g., if it is 1.7 or 1.8. The errors would seem to indicate the system version of Java is not the issue.

• R.