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 <ni...@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 <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
