..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 tudor3@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=247343with Virtualbox support, where I asked how to increase it, has not been very helpful.
Tudor
On 31 January 2013 18:42, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 nicks@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 bufferscached
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 nicks@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 freeMem: 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
> 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 > greve@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 > > > greve@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 > > > greve@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
> > > >