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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