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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, July 17, 2020 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu <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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