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Hi Douglas,
For the container, I am using version 6.0.0-min
The freesurfer on my computer is
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Thanks,
Ahmed
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Thursday, July 23, 2020 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct error {Disarmed}
CAUTION: External Sender
what version of freesurfer are you running?
On 7/17/2020 2:24 PM, Bahrani, Ahmed A. wrote:
External Email - Use Caution
Hi Douglas,
I am using the following:
Linux Redhat version 7.9
Singularity version 3.6.0
Freesurefer version 6.0.0-min (for containers)
I checked all the recon-all.log, and it looks like all of the old reports and I
could not find where the error report of the freesurefer save from the
container. I have checked the file output, and it does not have a
recall-all.log.
Thanks,
Ahmed
________________________________
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 Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 17, 2020 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct error
CAUTION: External Sender
What version are you running? Can you send the recon-all.log file?
On 7/16/2020 3:40 PM, Bahrani, Ahmed A. wrote:
External Email - Use Caution
Hello Freesurfer experts,
I have a question related to the singularity container to run a bash script
that contains a freesurfer's commend "nu_correct".
The singularity container only runs as a root user login and gives error as
shown below with a general user login.
==================================================================================
---Error message---
evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) ||
*posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running evaluate_field (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)
--------------------------------------------------------------------
---Error message---
ncvarput: ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running minccalc (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)
--------------------------------------------------------------------
Would you advise, please?
Thanks,
Ahmed
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