On Jun 14, 2021, at 11:11, Kaija Sander <kaija.sander@mail.mcgill.ca> wrote:

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Hello,

I just wanted to follow up on this issue as it seems other people experience problems with hippocampal subfields segmentation but not this same issue.

Does anyone please have any idea how to help??

Thank you very much,

Kaija

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kaija Sander <kaija.sander@mail.mcgill.ca>
Sent: 02 June 2021 14:15
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in hippocampal subfields longitudinal processing

 

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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 

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