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 <ni...@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 <ni...@nmr.mgh.harvard.edu> >> > wrote: >> > Tudor, Greg, and Petr, >> > >> > I'm currently attempting to replicate this problem. In the >> > meantime, >> > can you tell me which Windows and which VirtualBox version you >> > are >> > running this on? I'm at a loss as to why this build no longer >> > works. >> > >> > Nick >> > >> > >> > On Mon, 2013-01-28 at 18:19 +0000, Tudor Popescu wrote: >> > > Dear Nick, >> > > >> > > I was wondering whether you (or indeed anyone else reading >> > this!) know >> > > where the error that I report earlier in this thread might >> > be coming >> > > from. Many thanks in advance! >> > > >> > > Tudor >> > > >> > > On 20 December 2012 05:27, Douglas Greve >> > <gr...@nmr.mgh.harvard.edu> >> > > wrote: >> > > Hi Tudor, I don't know how to solve this problem. >> > Maybe Nick >> > > knows. >> > > doug >> > > >> > > >> > > On 12/19/12 6:59 AM, Tudor Popescu wrote: >> > > >> > > > Hi Doug, thanks for replying, here is the file >> > attached. In >> > > > case the attachment doesn't go through please let >> > me know >> > > > if I should send it to a different address. >> > > > Tudor >> > > > >> > > > On 18 December 2012 17:34, Douglas N Greve >> > > > <gr...@nmr.mgh.harvard.edu> wrote: >> > > > >> > > > Can you send the recon-all.log file >> > (located in the >> > > > subject/scripts folder). >> > > > doug >> > > > >> > > > >> > > > On 12/18/2012 11:41 AM, Tudor Popescu >> > wrote: >> > > > > Hello, >> > > > > >> > > > > First of all, apologies for asking for >> > help three >> > > > times today! THings >> > > > > will hopefully become clearer once I get >> > used to >> > > > FS a bit; I really do >> > > > > appreciate the amazing support provided >> > by the >> > > > team behind FreeSurfer! >> > > > > >> > > > > I ran the following command on one of my >> > > > structurals: >> > > > > >> > > > >> > > > > /recon-all -subject M01 -i M01.nii.gz >> > -all/ >> > > > > >> > > > > After a few minutes, recon-all ended >> > with the >> > > > following message: >> > > > > >> > > > >> > > > > /Assertion failed at line 827 in file >> > > > templates/CachedArray.cc/ >> > > > > /nu_estimate_np_and_em: crashed while >> > running >> > > > volume_stats >> > > > > (termination status=256)/ >> > > > > /nu_correct: crashed while running >> > > > nu_estimate_np_and_em (termination >> > > > > status=256)/ >> > > > > /ERROR: nu_correct/ >> > > > > /Linux FreeSurfer 2.6.28-11-generic >> > #42-Ubuntu SMP >> > > > Fri Apr 17 01:57:59 >> > > > > UTC 2009 i686 GNU/Linux/ >> > > > > >> > > > > I apologise for reporting an error >> > that's already >> > > > been reported in the >> > > > > past, but unfortunately the solutions >> > suggested in >> > > > those past threads >> > > > > did not work in my case. To address a >> > few of them: >> > > > > >> > > > >> > > > > * my PATH (listed below) does not seem >> > to >> > > > include two MNI installations >> > > > > >> > > > >> > >> //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ >> > > > > * the version of FreeSurfer that I >> > installed is >> > > > the latest disk >> > > > > image available on the website >> > > > > >> > > > >> > (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I >> > did >> > > > > not see any dev version that would >> > presumably >> > > > include any missing >> > > > > libraries presumably implied by the >> > above >> > > > error >> > > > > * I tried updating the Xubuntu inside >> > my >> > > > VirtualBox, however it >> > > > > reports an insufficient space >> > problem that >> > > > from I can see does not >> > > > > have a trivial fix >> > > > > >> > > > > Advance thanks for any help! >> > > > > Tudor >> > > > > >> > > > > >> > > > >> > > > > >> > _______________________________________________ >> > > > > Freesurfer mailing list >> > > > > Freesurfer@nmr.mgh.harvard.edu >> > > > > >> > > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > >> > > > -- >> > > > Douglas N. Greve, Ph.D. >> > > > MGH-NMR Center >> > > > gr...@nmr.mgh.harvard.edu >> > > > Phone Number: 617-724-2358 >> > > > Fax: 617-726-7422 >> > > > >> > > > Bugs: >> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > > > FileDrop: >> > > > >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > > > Outgoing: >> > > > >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > > > >> > > > >> > _______________________________________________ >> > > > Freesurfer mailing list >> > > > Freesurfer@nmr.mgh.harvard.edu >> > > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > >> > > > >> > > > The information in this e-mail is intended >> > only for >> > > > the person to whom it is >> > > > addressed. If you believe this e-mail was >> > sent to >> > > > you in error and the e-mail >> > > > contains patient information, please >> > contact the >> > > > Partners Compliance HelpLine at >> > > > http://www.partners.org/complianceline . >> > If the >> > > > e-mail was sent to you in error >> > > > but does not contain patient information, >> > please >> > > > contact the sender and properly >> > > > dispose of the e-mail. >> > > > >> > > > >> > > >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > >> >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
