Thanks Nick,
I ran the rm command and then re-ran recon-all. Got the same error, but at least now recon-all.log was created, see attached.
Tudor
On 31 January 2013 17:16, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
the log indicates that you need to run this:
rm /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh
to get recon-all to run again.
Nick
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 cachedMem: 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 freeMem: 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 > Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer