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 <tud...@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 > <ni...@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 > <ni...@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 > <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
