..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 > <https://forums.virtualbox.org/viewtopic.php?f=6&t=53861&p=247343>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 >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> > >> >> >
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