External Email - Use Caution        

To follow up on this, it seems the issue is related to where the data are stored on the user’s server and perhaps the filesystem/mode of access being used.  There does not seem to be any issue with Ubuntu generally, as processing works fine on the user’s OS drive…

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Jayasekera, Dinal" <dinal.jayasekera@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, April 11, 2019 at 12:11 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

        External Email - Use Caution        

Douglas,


I've run the recon-all script with images from patients that were previously run using FreeSurfer 5.3.0 and I received the same error. 


I haven't run it outside of the HCP pipeline. I can attempt that to see if it gives a different result. I'm not exactly sure how to go about doing this. Could you advise me on the best sequence of actions to take?


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, April 10, 2019 5:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0
 
Have you looked at the images to verify that there are no major problems
with it? Can you run it outside of the HCP pipeline to make sure it is
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
>         External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used
> FreeSurfer 6.0. I get the following error when running recon-all using
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on
> the same set of data. Are the MNI tools distributed through FreeSurfer
> 6.0 sensitive to the operating system and its version? Does anyone
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera <https://dinaljay.weebly.com/>*
> *
> *
> PhD Candidate | InSITE Fellow <https://www.insitefellows.org/>
> Ammar Hawasli Lab <https://hawaslilab.weebly.com/>
> Department of Biomedical Engineering
> <https://bme.wustl.edu/Pages/default.aspx> | Washington University in
> St. Louis <https://wustl.edu/>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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