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 <tud...@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 > <ni...@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 > <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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
