External Email - Use Caution 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 <fsbu...@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_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 > > <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/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 > > <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. >
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