Hi Pascale,

Maybe try setting the MCR_CACHE_ROOT env variable to somewhere under your user or project directory. It’s possible your OS is deleting the tmp directory after some time. What are the contents of $FREESURFER_HOME/build-stamp.txt?

Best

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pascale Patenaude <pascalepatenaude@hotmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, March 11, 2020 at 12:30 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in segmentSubjectT1_autoEstimateAlveusML

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Hello FreeSurfer developers,

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