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.eduwrote:
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.