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Oh my goodness silly me, I just realised where I went wrong... So sorry!
It does appear to be working now, so fingers crossed I can finish off my
subjects.
Thank you so much!!
Kaija
________________________________
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: 29 July 2021 18:20
To: Kaija Sander <kaija.san...@mail.mcgill.ca>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
The line of code you sent doesn’t seem changed though
best
andrew
From: Kaija Sander <kaija.san...@mail.mcgill.ca>
Date: Thursday, July 29, 2021 at 5:40 PM
To: Hoopes, Andrew <ahoo...@mgh.harvard.edu>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
External Email - Use Caution
Hi Andrew,
I just meant that upon going to make those changes, it appears the change has
already been made, therefore I am not entirely sure what the issue is...
Best,
Kaija
________________________________
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: 29 July 2021 16:45
To: Kaija Sander <kaija.san...@mail.mcgill.ca>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Cc: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
Hi Kaija,
Not sure I follow. Have you tried making the change I suggested in the last
email?
Best,
Andrew
From: Kaija Sander <kaija.san...@mail.mcgill.ca>
Date: Wednesday, July 28, 2021 at 2:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Hoopes, Andrew <ahoo...@mgh.harvard.edu>, Iglesias Gonzalez, Juan E.
<jiglesiasgonza...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
External Email - Use Caution
Hi Andrew and Eugenio,
Sorry for taking so long to follow up on this again, but after checking
MCR_CACHE_ROOT path, it seems that it has already been changed. It is currently
set to
MCR_CACHE_ROOT=$( echo "/tmp/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;
I'm not sure where I am going wrong...
Best,
Kaija
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew
<ahoo...@mgh.harvard.edu>
Sent: 23 June 2021 14:29
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
Hi Kaija,
I believe this is related to limitations in temporary file handling. You could
try manually replacing the MCR_CACHE_ROOT path on line 49 of:
$FREESURFER_HOME/bin/run_SegmentSubfieldsT1Longitudinal.sh
With something like:
MCR_CACHE_ROOT=$( echo "$HOME/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;
That seems to have fixed this problem in the past.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kaija Sander
<kaija.san...@mail.mcgill.ca>
Date: Monday, June 14, 2021 at 9:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
External Email - Use Caution
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan
E. <jiglesiasgonza...@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.san...@mail.mcgill.ca<mailto:kaija.san...@mail.mcgill.ca>> wrote:
External Email - Use Caution
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Kaija Sander
<kaija.san...@mail.mcgill.ca<mailto:kaija.san...@mail.mcgill.ca>>
Sent: 02 June 2021 14:15
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in hippocampal subfields longitudinal processing
External Email - Use Caution
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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