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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

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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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External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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}

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