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Actually the same error occurs with thalamus segmentation also. I made the change you suggested on resolution at the segmentHA_T1.sh (yet I was not allowed to make the change on the initial file so I created a new one) and now when I run the command it says: "permission denied”. I tried with sudo and it says “command not found”.

Any ideas on that? Thank you once again for your immediate response!

Georgia

On 18 Nov 2021, at 10:55 PM, Georgia Kapizioni geo.kapizioni@gmail.com wrote:

Thank you so much for your reply Eugenio.

I have 16 GB of RAM. Do you think this would be a problem?

Thanks again, Georgia

...

On 18 Nov 2021, at 10:04 PM, Georgia Kapizioni <geo.kapizioni@gmail.com mailto:geo.kapizioni@gmail.com> wrote:

Dear Freesurfer experts,

I am trying to run hippocampal subfields segmentation, using the command: segmentHA_T1.sh subject The analysis is running for approximately 20 mins and then the following error appears:

f this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1bAOeeu-yT9Ghsf3DgdHjQExvDxgifx7t9eLoK-E797kgPyu... http://secure-web.cisco.com/1bAOeeu-yT9Ghsf3DgdHjQExvDxgifx7t9eLoK-E797kgPyuk5FQHH64FDyPTOI9anMEuPHYLGqcKwvw5pevb7x89Fvhew6AZuZOi3AGkq1DT0qgzzIXlTNfTS_sQOTos2SMFSwo2ept162uhYGghknEloTanE0GpM9yRwLMcbiN3nG4LYjFlygvZts_rtH7LUhka6JhJOc9cGBy42DM5eT3x8RNgJUvWAMT6VO1jF9k5jN6I_bz7kJqopSLOOUXVlI-c37UfoKymMwXQSFuf0scRXho8Dvf7FyAE5PxHH8KtKhyolPV0MA3V6DpUcs6A/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /Users/theodore/matlab_crash_dump.4118-1 **

MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 4118 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML 6529 /Users/xxx/Downloads/xxx/qcache 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0 Darwin MacBook-Pro-Theodore.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET

Attached please also find the script output. I am using the 7. 1. version of FS.

Could you please help me resolve this issue? Thank you in advance, Georgia

<hippocampal-subfields-T1.log>