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Hello FreeSurfer Developers,
I'm attempting to segment thalamic nuclei, as described by the tutorial page (
https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb7YVmB72kOrHuNn1V8uoNhZN-KHe4ok9nSjzkSzoyH5n058ic0lLqwrMVHZ1ozpd7WV13-3izOOM4vTGZYclV0LEUE8KhAUx622iHqFKU9VFaY7mQtisbVEWK7YBKaAQw7RXbGIA71WJAz-5JKkJ0pl7BBS7MJrP4hFzbKx4mjI-PAgshzNpARL7zVl83KzC8c5y1v2hPafTqoIG4MC_6IeE6txqYTA7C8LF0xfIWg/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei),
but I got an Matlab routine error. I’t happened after the upgrade to MacOS Big Sur and I guess it is a compatibility issue. I tried also to re-install the routine (by fs_install_mcr R2014b
) and to run the process by docker container but the process ended with the same error.
(Obviously, I got the same error also trying the hippocampus&amygdala module).
ERROR:
MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_SegmentThalamicNuclei.sh: line 33: 3322 Killed: 9 /Applications/freesurfer/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei subjHC001/ /Applications/freesurfer/subjects 0.5 /Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasMesh.gz
/Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr /Applications/freesurfer/bin/' 1 0
Darwin iMac-di-Daniela.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64
I've searched the list and I didn’t found a way to fix it.
Does anyone have any thoughts on how to trouble-shoot this one?
Also, Ive attached the thalamic-nuclei-mainFreeSurferT1.log in case it's of any use.
Thanks in advance
Best regards,
Daniela