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 mailto: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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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.
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.
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
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
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 > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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
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
Tudor,
I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM.
I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation.
Nick
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 bufferscached
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 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
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 versionyou
are running this on? I'm at a loss as to why this build nolonger
works. Nick On Mon, 2013-01-28 at 18:19 +0000, Tudor Popescu wrote: > Dear Nick, > > I was wondering whether you (or indeed anyone elsereading
this!) know > where the error that I report earlier in this threadmight
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 pleaselet
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 askingfor
help three > > times today! THings > > > will hopefully become clearer once Iget
used to > > FS a bit; I really do > > > appreciate the amazing supportprovided
by the > > team behind FreeSurfer! > > > > > > I ran the following command on one ofmy
> > 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 notseem
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 thatwould
presumably > > include any missing > > > libraries presumably implied bythe
above > > error > > > * I tried updating the Xubuntuinside
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 isintended
only for > > the person to whom it is > > addressed. If you believe this e-mailwas
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 patientinformation,
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
Hi NIck,
I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space:
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
The list of commands I ran were: *sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all*
THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion https://forums.virtualbox.org/viewtopic.php?f=6&t=53861&p=247343with Virtualbox support, where I asked how to increase it, has not been very helpful.
Tudor
On 31 January 2013 18:42, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM.
I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation.
Nick
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 bufferscached
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 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
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 versionyou
are running this on? I'm at a loss as to why this build nolonger
works. Nick On Mon, 2013-01-28 at 18:19 +0000, Tudor Popescu wrote: > Dear Nick, > > I was wondering whether you (or indeed anyone elsereading
this!) know > where the error that I report earlier in this threadmight
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 pleaselet
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 askingfor
help three > > times today! THings > > > will hopefully become clearer once Iget
used to > > FS a bit; I really do > > > appreciate the amazing supportprovided
by the > > team behind FreeSurfer! > > > > > > I ran the following command on one ofmy
> > 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 notseem
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 thatwould
presumably > > include any missing > > > libraries presumably implied bythe
above > > error > > > * I tried updating the Xubuntuinside
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 isintended
only for > > the person to whom it is > > addressed. If you believe this e-mailwas
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 patientinformation,
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
..I also did the following in the meantime, to make sure that the problem isn't due to a path error: - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, and they return their version number - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point into $FREESURFER_HOME/mni , as they should
Still cannot get recon-all to run because of the error mentioned previously & currently at my wit's end! :(
On 4 February 2013 10:29, Tudor Popescu tudor3@gmail.com wrote:
Hi NIck,
I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space:
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
The list of commands I ran were: *sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all*
THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion https://forums.virtualbox.org/viewtopic.php?f=6&t=53861&p=247343with Virtualbox support, where I asked how to increase it, has not been very helpful.
Tudor
On 31 January 2013 18:42, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Tudor,
I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM.
I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation.
Nick
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 bufferscached
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 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
> 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
> > > >
Tudor,
Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution.
Nick
On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote:
..I also did the following in the meantime, to make sure that the problem isn't due to a path error:
- ran nu_estimate_np_and_em and nu_correct: both seem to respond fine,
and they return their version number
- checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point
into $FREESURFER_HOME/mni , as they should
Still cannot get recon-all to run because of the error mentioned previously & currently at my wit's end! :(
On 4 February 2013 10:29, Tudor Popescu tudor3@gmail.com wrote: Hi NIck,
I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space: FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell The list of commands I ran were: sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion with Virtualbox support, where I asked how to increase it, has not been very helpful. Tudor On 31 January 2013 18:42, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM. I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation. Nick > 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 >> 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 >> >> > > Freesurfer@nmr.mgh.harvard.edu >> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >> >> > >> >> > >> >> > >> >> >> >> >> >> >> > >> >> >
Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution.
Nick
On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote:
..I also did the following in the meantime, to make sure that the problem isn't due to a path error:
- ran nu_estimate_np_and_em and nu_correct: both seem to respond fine,
and they return their version number
- checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point
into $FREESURFER_HOME/mni , as they should
Still cannot get recon-all to run because of the error mentioned previously & currently at my wit's end! :(
On 4 February 2013 10:29, Tudor Popescu tudor3@gmail.com wrote: Hi NIck,
I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space: FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell The list of commands I ran were: sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion with Virtualbox support, where I asked how to increase it, has not been very helpful. Tudor On 31 January 2013 18:42, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM. I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation. Nick > 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 >> 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 >> >> > > Freesurfer@nmr.mgh.harvard.edu >> >> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > >> >> > >> >> > >> >> > >> >> >> >> >> >> >> > >> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote:
Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Tudor,
Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution.
Nick
On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote:
..I also did the following in the meantime, to make sure that the problem isn't due to a path error:
- ran nu_estimate_np_and_em and nu_correct: both seem to respond fine,
and they return their version number
- checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point
into $FREESURFER_HOME/mni , as they should
Still cannot get recon-all to run because of the error mentioned previously & currently at my wit's end! :(
On 4 February 2013 10:29, Tudor Popescu tudor3@gmail.com wrote: Hi NIck,
I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space: FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell The list of commands I ran were: sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion with Virtualbox support, where I asked how to increase it, has not been very helpful. Tudor On 31 January 2013 18:42, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM. I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation. Nick > 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 >> 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 >> >> > > Freesurfer@nmr.mgh.harvard.edu >> >> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> > >> >> > >> >> > >> >> > >> >> >> >> >> >> >> > >> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, to make sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be an issue, however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used Avail Use% Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1% /lib/modules/2.6.28-11-generic/volatile > overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs > recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB free space, and the > discussion with Virtualbox support, where I asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in the fsv5.1 WindowsVM. > > I noticed though that it appears you have the buckner > tutorial data. I > dont have my virtual machine on hand to check the > available disk space > reserved for it, but check that you have enough disk > space. run 'df -h'. > or just delete some of the tutorial subjects and try > again. This might be > the problem since you mentioned you were having > problems with > recon-all.log file creation. > > Nick > > > > 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 > >> 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 > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has 0KB available space, due to the way the FS/Virtualbox drive was created (i.e. size-tailored to the FS installation). My files were in the folder that I shared through Virtualbox though (/media/Dell), which has plenty of space available, and that's where I ran recon-all from! Shouldn't I have
2GB of space in *that* folder? If not, then the issue of making space
available in the home drive (or whatver it's called), i.e. in /dev/sda1, is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum.
Output of df -h below.
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
On 13 February 2013 20:47, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, to make sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be an issue, however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used Avail Use% Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1% /lib/modules/2.6.28-11-generic/volatile > overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs > recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB free space, and the > discussion with Virtualbox support, where I asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in the fsv5.1 WindowsVM. > > I noticed though that it appears you have the buckner > tutorial data. I > dont have my virtual machine on hand to check the > available disk space > reserved for it, but check that you have enough disk > space. run 'df -h'. > or just delete some of the tutorial subjects and try > again. This might be > the problem since you mentioned you were having > problems with > recon-all.log file creation. > > Nick > > > > 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 > >> 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 > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle.
Nick
Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has 0KB available space, due to the way the FS/Virtualbox drive was created (i.e. size-tailored to the FS installation). My files were in the folder that I shared through Virtualbox though (/media/Dell), which has plenty of space available, and that's where I ran recon-all from! Shouldn't I have
2GB of space in *that* folder? If not, then the issue of making space
available in the home drive (or whatver it's called), i.e. in /dev/sda1, is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum.
Output of df -h below.
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
On 13 February 2013 20:47, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, to make sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be an issue, however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used Avail Use% Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1% /lib/modules/2.6.28-11-generic/volatile > overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR/media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB free space, and the > discussion with Virtualbox support, where I asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in the fsv5.1 WindowsVM. > > I noticed though that it appears you have the buckner > tutorial data. I > dont have my virtual machine on hand to check the > available disk space > reserved for it, but check that you have enough disk > space. run 'df -h'. > or just delete some of the tutorial subjects and try > again. This might be > the problem since you mentioned you were having > problems with > recon-all.log file creation. > > Nick > > > > 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 > >> 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 > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I don't think there *is* any free space on the virtualbox ubuntu disk - that disk would presumably correspond to the first row in the "df -h" output, which shows as 0 free space. So even for recon-alls ran on data located on external HDDs, I would expect the nu_correct error to come up on all FS/VirtualBox installations, assuming that tmp space is a requirement (which makes sense).
However, you mentioned at some point that bert runs to completion in the fsv5.1 WindowsVM for other users, which is intriguing...
Tudor
On 14 February 2013 15:29, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle.
Nick
Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has 0KB available space, due to the way the FS/Virtualbox drive was created (i.e. size-tailored to the FS installation). My files were in the folder that I shared through Virtualbox though (/media/Dell), which has plenty
of
space available, and that's where I ran recon-all from! Shouldn't I have
2GB of space in *that* folder? If not, then the issue of making space
available in the home drive (or whatver it's called), i.e. in /dev/sda1, is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum.
Output of df -h below.
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
On 13 February 2013 20:47, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor
On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, to make sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be an issue, however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used Avail Use% Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1% /lib/modules/2.6.28-11-generic/volatile > overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR/media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB free space, and the > discussion with Virtualbox support, where I asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in the fsv5.1 WindowsVM. > > I noticed though that it appears you have the buckner > tutorial data. I > dont have my virtual machine on hand to check the > available disk space > reserved for it, but check that you have enough disk > space. run 'df -h'. > or just delete some of the tutorial subjects and try > again. This might be > the problem since you mentioned you were having > problems with > recon-all.log file creation. > > Nick > > > > 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 > >> 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 > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Tudor,
In the default installation, there should be 2GB of free space on the default disk, so somehow it got filled. Try deleting unnecessary stuff (packages added during an upgrade I think mentioned doing, or subjects in the freesurfer/subjects dir). Freeing just a few tens of MB should be enough to get things working again.
Nick
Hi Nick,
I don't think there *is* any free space on the virtualbox ubuntu disk - that disk would presumably correspond to the first row in the "df -h" output, which shows as 0 free space. So even for recon-alls ran on data located on external HDDs, I would expect the nu_correct error to come up on all FS/VirtualBox installations, assuming that tmp space is a requirement (which makes sense).
However, you mentioned at some point that bert runs to completion in the fsv5.1 WindowsVM for other users, which is intriguing...
Tudor
On 14 February 2013 15:29, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle.
Nick
Thanks Nick, it seems disk space is the issue after all, as /dev/sda1
has
0KB available space, due to the way the FS/Virtualbox drive was
created
(i.e. size-tailored to the FS installation). My files were in the
folder
that I shared through Virtualbox though (/media/Dell), which has
plenty of
space available, and that's where I ran recon-all from! Shouldn't I
have
2GB of space in *that* folder? If not, then the issue of making space
available in the home drive (or whatver it's called), i.e. in
/dev/sda1,
is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum.
Output of df -h below.
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
On 13 February 2013 20:47, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me
to
try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the
baseline
(bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain
the
exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's
VMWare
to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my
OS
(Win XP) is 32 bit. Is there nothing else I can try?Searching
the list for error messages related to those nu_components,
it seems that many people have had this problem before.Were
most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successfulinstallation
of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, tomake
sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be anissue,
however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used AvailUse%
Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1%/lib/modules/2.6.28-11-generic/volatile
> overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR/media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB freespace,
and the > discussion with Virtualbox support, whereI
asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in thefsv5.1
WindowsVM. > > I noticed though that it appearsyou
have the buckner > tutorial data. I > dont have my virtual machine onhand
to check the > available disk space > reserved for it, but check thatyou
have enough disk > space. run 'df -h'. > or just delete some of thetutorial
subjects and try > again. This might be > the problem since you mentionedyou
were having > problems with > recon-all.log file creation. > > Nick > > > > 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 youneed
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: > >> > > >> > totalused
free > shared buffers > >> cached > >> > Mem: 2838372522304
2316068 > 0 11176 > >> 37663 > >> > > >> > Virtualbox support advisedme
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 outputdoes
not, for some > reason, get written to > >> the > >> > recon-all.log file inside\bert
\scripts. I > deleted the file hoping it > >> > would > >> > be automatically recreatedat
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 havea
very long output > from the Terminal (I > >> also > >> > added -debug to thecommand),
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 thedistribution,
and nuintensitycor > is the stage that > >> runs > >> >> nu_correct. > >> >> > >> >> I noticed in your recon-all.log file this line: > >> >> > >> >> totalused
free > >> >> Mem: 1026680673692
352988 > >> >> > >> >> which means only 353KB of memory is available > for freesurfer. this > >> is > >> >> way too low. freesurferneeds
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 terminalto
get the available > memory under the > >> 'free' > >> >> column. confirm that 'recon-all -s bert -all' > runs successfully for > >> you > >> >> prior to runningunknown/new
data. > >> >> > >> >> Nick > >> >> > >> >> > >> >> On Mon, 2013-01-28 at 19:01 +0000, Tudor Popescu > wrote: > >> >> > Hi Nick, > >> >> > > >> >> > Thanks for your help, I'mon
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. Manythanks
in advance! > >> >> > > > >> >> > > Tudor > >> >> > > > >> >> > > On 20 December 2012 05:27, Douglas > Greve > >> >> > <greve@nmr.mgh.harvard.edu> > >> >> > > wrote: > >> >> > > HiTudor,
I don't know how > to solve this problem. > >> >> > Maybe Nick > >> >> > > knows. > >> >> > > doug > >> >> > > > >> >> > > > >> >> > > On 12/19/12 6:59 AM, Tudor > Popescu wrote: > >> >> > > > >> >> > > > HiDoug,
thanks for > replying, here is the file > >> >> > attached. In > >> >> > > > casethe
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. > >> >> > > > > >> >> > > > > >> >> > > > >> >> > > > >> >> > > > >> >> > > > _______________________________________________ > >> >> > > Freesurfermailing
list > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I'm afraid this didn't work either. I deleted the Subjects folder inside /freesurfer, which freed up 1.3GB on the /dev/sda1. All other drives had enough space available:
*> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 8.6G 1.3G 88% / tmpfs 1.2G 0 1.2G 0% /lib/init/rw varrun 1.2G 108K 1.2G 1% /var/run varlock 1.2G 0 1.2G 0% /var/lock udev 1.2G 152K 1.2G 1% /dev tmpfs 1.2G 0 1.2G 0% /dev/shm lrm 1.2G 2.4M 1.2G 1% /lib/modules/2.6.28-11-generic/volatile Dell 173G 84G 90G 49% /media/Dell*
Memory seemed fine as well: *
free
total used free shared buffers cached Mem: 2447088 870828 1576260 0 345228 379444 -/+ buffers/cache: 146156 2300932 Swap: 530104 0 530104*
Even so, the same error occurred:
*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*
I know you too must be at your wit's end, but .. anything else you can think of to try and make this work? Log files are attached.
many thanks! Tudor
On 14 February 2013 20:34, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
In the default installation, there should be 2GB of free space on the default disk, so somehow it got filled. Try deleting unnecessary stuff (packages added during an upgrade I think mentioned doing, or subjects in the freesurfer/subjects dir). Freeing just a few tens of MB should be enough to get things working again.
Nick
Hi Nick,
I don't think there *is* any free space on the virtualbox ubuntu disk - that disk would presumably correspond to the first row in the "df -h" output, which shows as 0 free space. So even for recon-alls ran on data located on external HDDs, I would expect the nu_correct error to come up on all FS/VirtualBox installations, assuming that tmp space is a requirement (which makes sense).
However, you mentioned at some point that bert runs to completion in the fsv5.1 WindowsVM for other users, which is intriguing...
Tudor
On 14 February 2013 15:29, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle.
Nick
Thanks Nick, it seems disk space is the issue after all, as /dev/sda1
has
0KB available space, due to the way the FS/Virtualbox drive was
created
(i.e. size-tailored to the FS installation). My files were in the
folder
that I shared through Virtualbox though (/media/Dell), which has
plenty of
space available, and that's where I ran recon-all from! Shouldn't I
have
2GB of space in *that* folder? If not, then the issue of making space
available in the home drive (or whatver it's called), i.e. in
/dev/sda1,
is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum.
Output of df -h below.
*FreeSurfer:~> df -h Filesystem Size Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun 755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell*
On 13 February 2013 20:47, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Tudor,
I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space.
Nick
On Wed, 2013-02-13 at 18:32 +0000, Tudor Popescu wrote:
Hi Nick,
I was wondering if there might be any other solutions left for me
to
try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the
baseline
(bert) command past that nu_correct error.
In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain
the
exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's
VMWare
to use on the 64-bit OS, as you suggested, however their website is down at the moment.
Many thanks for your help.
Tudor
On 6 February 2013 16:12, Tudor Popescu tudor3@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my
OS
(Win XP) is 32 bit. Is there nothing else I can try?Searching
the list for error messages related to those nu_components,
it seems that many people have had this problem before.Were
most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor On 6 February 2013 16:06, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successfulinstallation
of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +0000, Tudor Popescu wrote: > ..I also did the following in the meantime, tomake
sure that the > problem isn't due to a path error: > - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, > and they return their version number > - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point > into $FREESURFER_HOME/mni , as they should > > Still cannot get recon-all to run because of the error mentioned > previously & currently at my wit's end! :( > > On 4 February 2013 10:29, Tudor Popescu <tudor3@gmail.com> wrote: > Hi NIck, > > I too thought disk space might be anissue,
however I''ve been > running the recon-all from a mounted partition (shared folder > in Virtualbox) that has plenty of space: > > FreeSurfer:~> df -h > Filesystem Size Used AvailUse%
Mounted on > /dev/sda1 11G 9.8G 0 100% / > tmpfs 755M 0 755M 0% /lib/init/rw > varrun 755M 104K 754M 1% /var/run > varlock 755M 0 755M 0% /var/lock > udev 755M 152K 754M 1% /dev > tmpfs 755M 0 755M 0% /dev/shm > lrm 755M 2.4M 752M > 1%/lib/modules/2.6.28-11-generic/volatile
> overflow 1.0M 12K 1012K 2% /tmp > Dell 173G 106G 68G 62% /media/Dell > > > The list of commands I ran were: > sudo mount -t vboxsf Dell /media/Dell > setenv > SUBJECTS_DIR/media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all > > THis is because running it from the home (default) partition > was not possible, as it has 0 KB freespace,
and the > discussion with Virtualbox support, whereI
asked how to > increase it, has not been very helpful. > > Tudor > > > On 31 January 2013 18:42, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > Tudor, > > I'm a bit at a loss as to why it wont work. It appears > you have plenty of > available memory. Also, another person on the list > confirmed that bert > will run to completion in thefsv5.1
WindowsVM. > > I noticed though that it appearsyou
have the buckner > tutorial data. I > dont have my virtual machine onhand
to check the > available disk space > reserved for it, but check thatyou
have enough disk > space. run 'df -h'. > or just delete some of thetutorial
subjects and try > again. This might be > the problem since you mentionedyou
were having > problems with > recon-all.log file creation. > > Nick > > > > 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 youneed
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: > >> > > >> > totalused
free > shared buffers > >> cached > >> > Mem: 2838372522304
2316068 > 0 11176 > >> 37663 > >> > > >> > Virtualbox support advisedme
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 outputdoes
not, for some > reason, get written to > >> the > >> > recon-all.log file inside\bert
\scripts. I > deleted the file hoping it > >> > would > >> > be automatically recreatedat
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 havea
very long output > from the Terminal (I > >> also > >> > added -debug to thecommand),
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 thedistribution,
and nuintensitycor > is the stage that > >> runs > >> >> nu_correct. > >> >> > >> >> I noticed in your recon-all.log file this line: > >> >> > >> >> totalused
free > >> >> Mem: 1026680673692
352988 > >> >> > >> >> which means only 353KB of memory is available > for freesurfer. this > >> is > >> >> way too low. freesurferneeds
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 terminalto
get the available > memory under the > >> 'free' > >> >> column. confirm that 'recon-all -s bert -all' > runs successfully for > >> you > >> >> prior to runningunknown/new
data. > >> >> > >> >> Nick > >> >> > >> >> > >> >> On Mon, 2013-01-28 at 19:01 +0000, Tudor Popescu > wrote: > >> >> > Hi Nick, > >> >> > > >> >> > Thanks for your help, I'mon
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. Manythanks
in advance! > >> >> > > > >> >> > > Tudor > >> >> > > > >> >> > > On 20 December 2012 05:27, Douglas > Greve > >> >> > <greve@nmr.mgh.harvard.edu> > >> >> > > wrote: > >> >> > > HiTudor,
I don't know how > to solve this problem. > >> >> > Maybe Nick > >> >> > > knows. > >> >> > > doug > >> >> > > > >> >> > > > >> >> > > On 12/19/12 6:59 AM, Tudor > Popescu wrote: > >> >> > > > >> >> > > > HiDoug,
thanks for > replying, here is the file > >> >> > attached. In > >> >> > > > casethe
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. > >> >> > > > > >> >> > > > > >> >> > > > >> >> > > > >> >> > > > >> >> > > > _______________________________________________ > >> >> > > Freesurfermailing
list > >> >> > > Freesurfer@nmr.mgh.harvard.edu > >> >> > > > >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> > > >> > >> > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Nick Schmansky -
Tudor Popescu