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Hi Eugenio,

No problem at all, thanks for getting back to me!
All the subjects should have been acquired exactly the same way with the same parameters, so I don't understand... So far I've only gotten through a few subjects but decided to reach out when I realised it happened to at least 3 of them (out of 7 so far, 18 total). I did run one of the subjects multiple times, and even re-ran the recon-all and still got the exact same error.

I am very puzzled!

Thanks so much,
Kaija
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: 14 June 2021 14:20
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
 
Sorry for not having replied earlier, Kaija.
This is very strange. Do these subjects have more time points or a larger field of view? Did you run all the subjects on the same platform? Is the issue with these few subjects reproducible?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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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
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
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