I’m trying to run thesegment_T1.sh command on centos 7 in docker (fs 7.2.0). I have matlab v2014b installed in fs there. The subjects were successfully put through recon-all on mac Big Sur (also fs 7.2.0 but matlab does not want to work with Big Sur). I don’t know what to do with the error I get with every recon-all’d subject:

Smoothing mesh collection with kernel size 0.750000 ...Smoothing class: 0

/usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40:   797 Killed                  /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML bmat1 /usr/local/freesurfer/subjects 0.333333333333333333333333333333333333 /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr /usr/local/freesurfer/bin/' 0

Linux 3520b46e7a14 5.10.47-linuxkit #1 SMP Sat Jul 3 21:51:47 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Thu Sep 16 23:20:28 UTC 2021

For more details, see the log file /usr/local/freesurfer/subjects/bmat1/scripts/hippocampal-subfields-T1.log

If any one of you has run into this kind of problem or know how to solve it, I’d be happy to hear your thoughts.

Kind regards,

Agata