Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

Tudor, Greg, and Petr,

I'm currently attempting to replicate this problem. In the meantime, can you tell me which Windows and which VirtualBox version you are running this on? I'm at a loss as to why this build no longer works.

Nick

On Mon, 2013-01-28 at 18:19 +0000, Tudor Popescu wrote:

Dear Nick,

I was wondering whether you (or indeed anyone else reading this!) know where the error that I report earlier in this thread might be coming from. Many thanks in advance!

Tudor

On 20 December 2012 05:27, Douglas Greve greve@nmr.mgh.harvard.edu wrote: Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug

    On 12/19/12 6:59 AM, Tudor Popescu wrote:

    > Hi Doug, thanks for replying, here is the file attached. In
    > case the attachment doesn't go through  please let me know
    > if I should send it to a different address.
    > Tudor
    > 
    > On 18 December 2012 17:34, Douglas N Greve
    > <greve@nmr.mgh.harvard.edu> wrote:
    >         
    >         Can you send the recon-all.log file (located in the
    >         subject/scripts folder).
    >         doug
    >         
    >         
    >         On 12/18/2012 11:41 AM, Tudor Popescu wrote:
    >         > Hello,
    >         >
    >         > First of all, apologies for asking for help three
    >         times today! THings
    >         > will hopefully become clearer once I get used to
    >         FS a bit; I really do
    >         > appreciate the amazing support provided by the
    >         team behind FreeSurfer!
    >         >
    >         > I ran the following command on one of my
    >         structurals:
    >         >
    >         
    >         > /recon-all -subject M01 -i M01.nii.gz -all/
    >         >
    >         > After a few minutes, recon-all ended with the
    >         following message:
    >         >
    >         
    >         > /Assertion failed at line 827 in file
    >         templates/CachedArray.cc/
    >         > /nu_estimate_np_and_em: crashed while running
    >         volume_stats
    >         > (termination status=256)/
    >         > /nu_correct: crashed while running
    >         nu_estimate_np_and_em (termination
    >         > status=256)/
    >         > /ERROR: nu_correct/
    >         > /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP
    >         Fri Apr 17 01:57:59
    >         > UTC 2009 i686 GNU/Linux/
    >         >
    >         > I apologise for reporting an error that's already
    >         been reported in the
    >         > past, but unfortunately the solutions suggested in
    >         those past threads
    >         > did not work in my case. To address a few of them:
    >         >
    >         
    >         >   * my PATH (listed below) does not seem to
    >         include two MNI installations
    >         >
    >           //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/
    >         >   * the version of FreeSurfer that I installed is
    >         the latest disk
    >         >     image available on the website
    >         >
    >         (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did
    >         >     not see any dev version that would presumably
    >         include any missing
    >         >     libraries presumably implied by the above
    >         error
    >         >   * I tried updating the Xubuntu inside my
    >         VirtualBox, however it
    >         >     reports an insufficient space problem that
    >         from I can see does not
    >         >     have a trivial fix
    >         >
    >         > Advance thanks for any help!
    >         > Tudor
    >         >
    >         >
    >         
    >         > _______________________________________________
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    >         
    >         --
    >         Douglas N. Greve, Ph.D.
    >         MGH-NMR Center
    >         greve@nmr.mgh.harvard.edu
    >         Phone Number: 617-724-2358
    >         Fax: 617-726-7422
    >         
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    >         Outgoing:
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    >         
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