Tudor,

In the default installation, there should be 2GB of free space on the
default disk, so somehow it got filled.  Try deleting unnecessary stuff
(packages added during an upgrade I think mentioned doing, or subjects in
the freesurfer/subjects dir).  Freeing just a few tens of MB should be
enough to get things working again.

Nick

> Hi Nick,
>
> I don't think there *is* any free space on the virtualbox ubuntu disk -
> that disk would presumably correspond to the first row in the "df -h"
> output, which shows as 0 free space. So even for recon-alls ran on data
> located on external HDDs, I would expect the nu_correct error to come up
> on
> all FS/VirtualBox installations, assuming that tmp space is a requirement
> (which makes sense).
>
> However, you mentioned at some point that bert runs to completion in the
> fsv5.1 WindowsVM for other users, which is intriguing...
>
> Tudor
>
>
>
> On 14 February 2013 15:29, Nick Schmansky <ni...@nmr.mgh.harvard.edu>
> wrote:
>
>> Tudor,
>>
>> Now that there is free space on the virtualbox ubuntu disk, are you able
>> to complete recon-all's on data that is located on your external disk?
>> I
>> ask because although i'm not certain, i think nu_correct uses tmp space
>> on
>> the ubuntu local drive, which if it was full would cause recon failure
>> on
>> external data.  Thats my theory anyway.  We no longer have our local
>> VirtualBox expert that created this to support this issue, so this might
>> take some struggle.
>>
>> Nick
>>
>>
>> > Thanks Nick, it seems disk space is the issue after all, as /dev/sda1
>> has
>> > 0KB available space, due to the way the FS/Virtualbox drive was
>> created
>> > (i.e. size-tailored to the FS installation). My files were in the
>> folder
>> > that I shared through Virtualbox though (/media/Dell), which has
>> plenty
>> of
>> > space available, and that's where I ran recon-all from! Shouldn't I
>> have
>> >>2GB of space in *that* folder? If not, then the issue of making space
>> > available in the home drive (or whatver it's called), i.e. in
>> /dev/sda1,
>> > is, as it seems, a very non-trivial issue, which I have unsuccessfully
>> > tried to seek help with on the Virtualbox forum.
>> >
>> > Output of df -h below.
>> >
>> > *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*
>> >
>> > On 13 February 2013 20:47, Nick Schmansky <ni...@nmr.mgh.harvard.edu>
>> > wrote:
>> >
>> >> Tudor,
>> >>
>> >> I dont have any other suggestions, other than to make sure, as i
>> >> mentioned before, then you have free space on the disk that appears
>> >> within Xubuntu.  That is, from a terminal, when you type:
>> >>
>> >> df -h
>> >>
>> >> you should see that /dev/sda1 has about 2GB of space. the nu_correct
>> >> tools will fail if there is not enough disk space.
>> >>
>> >> Nick
>> >>
>> >>
>> >> 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 <tud...@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
>> >> >         <ni...@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
>> >> >                 <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 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
>> >> >                 >                 >> >> >
>> >> >                 >                 >> >> >
>> >> >                 >                 >> >> >
>> >> >                 >                 >> >> >
>> >> >                 >                 >> >>
>> >> >                 >                 >> >>
>> >> >                 >                 >> >>
>> >> >                 >                 >> >
>> >> >                 >                 >>
>> >> >                 >                 >>
>> >> >                 >                 >
>> >> >                 >
>> >> >                 >
>> >> >                 >
>> >> >                 >
>> >> >                 >
>> >> >
>> >> >
>> >> >                 _______________________________________________
>> >> >                 Freesurfer mailing list
>> >> >                 Freesurfer@nmr.mgh.harvard.edu
>> >> >
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >
>> >> >
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>>
>>
>

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