6 Feb
2013
6 Feb
'13
11:06 a.m.
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 >> >> > >> >> > >> >> > >> >> > >> >> >> >> >> >> >> > >> >> >