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 <
tudor3@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
> <
nicks@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
> <
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
> > 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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>
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>
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