I was able to verify that 'recon-all -s bert -nuintensitycor' works on
the windows virtualbox instance of fs5.1. bert is the sample data that
comes with the distribution, and nuintensitycor is the stage that runs
nu_correct.
I noticed in your recon-all.log file this line:
total used free
Mem: 1026680 673692 352988
which means only 353KB of memory is available for freesurfer. this is
way too low. freesurfer needs ideally 4GB, but at least 2GB. make sure
when you create the new instance in virtual box that you give it the
maximum memory your system allows. this means your windows machine
should have at least 4GB, ideally 6-8GB (because windows will take 2GB,
and xubuntu will take 1GB).
type 'free' in the terminal to get the available memory under the 'free'
column. confirm that 'recon-all -s bert -all' runs successfully for you
prior to running unknown/new data.
Nick
On Mon, 2013-01-28 at 19:01 +0000, Tudor Popescu wrote:
> Hi Nick,
>
> Thanks for your help, I'm on Windows XP SP3 & VirtualBox 4.2.4
>
> Tudor
>
> On 28 January 2013 18:30, Nick Schmansky <ni...@nmr.mgh.harvard.edu>
> wrote:
> 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
> <gr...@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
> > > <gr...@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
> > > >
> > > >
> > >
> > > >
> _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop:
> > >
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing:
> > >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > >
> _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > The information in this e-mail is intended
> only for
> > > the person to whom it is
> > > addressed. If you believe this e-mail was
> sent to
> > > you in error and the e-mail
> > > contains patient information, please
> contact the
> > > Partners Compliance HelpLine at
> > > http://www.partners.org/complianceline .
> If the
> > > e-mail was sent to you in error
> > > but does not contain patient information,
> please
> > > contact the sender and properly
> > > dispose of the e-mail.
> > >
> > >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
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