Hi Daniel This error is intriguing because the code did run for a while… Is it possible that you ran out of RAM memory? How much RAM does your machine have? (you can find it by clicking on the apple on the top left corner and then “about this Mac”) Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

On Jul 16, 2021, at 07:08, Daniela Vecchio <vecchio.dani@gmail.commailto:vecchio.dani@gmail.com> wrote:

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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/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb7...), 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

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