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-boun...@nmr.mgh.harvard.edu> on behalf of Pascale Patenaude
<pascalepatena...@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/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
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