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

External Email - Use Caution 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/HippocampalSubfieldsAndNucleiOfAmy...) 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