When trying to run segmentHA_T1.sh with the dev version of FreeSurfer to accomplish hippocampal subfield and amygdala subnuclei segmentation (see FreeSurfer module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) I get this error:

Open file failed because file '/tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.'

Attempt to execute SCRIPT kvlWriteImage as a function:

/tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m

Error in segmentSubjectT1_autoEstimateAlveusML (line 1547)

This tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs directory does not exist. I also have the matlab runtime required for this FreeSurfer module installed.

Does anyone have any suggestions on how this can be fixed?

Thank you in advance,

Pascale