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Hello all,
I am attempting to obtain the hippocampal subfields segmentation in a small longitudinal dataset (18 participants, 2 time points each). I have successfully been able to run recon-all, recon-all -base and recon-all -long (or at least, these steps appear to be completed without errors). However, when trying to run segmentHA_T1_long.sh, I encountering the following error (I have also attached the full log file of one of the subjects):
Open file failed because file '/tmp/MCR_511464988/.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.' The file "/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m" cannot be executed.
Error in SegmentSubfieldsT1Longitudinal (line 1795)
What is strange is that this has only happened for a couple of subjects, and has worked fine for the few others I did.
Does anyone have any suggestions of what might be going wrong and how to fix it?
Thank you very much, Kaija
FreeSurfer version: freesurfer-local-build-dev-20200116 Platform: Ubuntu 18.04.5