> Hi Nick,
>
> Thanks for your reply! I increased the memory available to FS in the
> virtualbox to the maximum allowed value (80% of my machine's total RAM),
> such that the free command returns:
>
> total used free shared buffers cached
> Mem: 2838372 522304 2316068 0 11176 37663
>
> Virtualbox support advised me to not increase this memory to more than 1GB
> (of my total 4GB), as this would lead to system instability. I tried it
> nonetheless, but even so, running "recon-all -s bert -all" still gives me
> the same error as before, which is presumably still memory-related.
>
> Unfortunately, the output does not, for some reason, get written to the
> recon-all.log file inside \bert\scripts. I deleted the file hoping it
> would
> be automatically recreated at the next call of recon-all, but it did not.
> I
> also then manually created a file with that name, but nothing got recorded
> in it. Therefore, I now have a very long output from the Terminal (I also
> added -debug to the command), which I can only show you by copying all the
> (truncated) text from the terminal window and pasting into the attached
> text file.
>
> Tudor
>
> On 29 January 2013 01:11, Nick Schmansky <
nicks@nmr.mgh.harvard.edu>
> wrote:
>
>> 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 <
nicks@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
>> > <
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
>> > > > >
>> > > > >
>> > > >
>> > > > >
>> > _______________________________________________
>> > > > > 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
>> > > >
greve@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
>> > >
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>> > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>> >
>>
>>
>>
>