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 <
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 with 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.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
> <
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 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
> <
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 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
> >> <
nicks@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
> >> >> > <
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
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> >> >> > > >
>
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> >> .
> >> >> > If the
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> >> >> > >
> >> >> > >
> >> >> > >
> _______________________________________________
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> >> >> > >
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> >> >> > >
> >>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >
> >>
> >>
> >
>
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