Hi Negar,

from your log file:
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 
i686 GNU/Linux

So it looks like you are running the 32bit free surfer version which will be 
limited to >= 4GB addressable memory, most likely only 2GB. You might want to 
try again using:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz
That way your memory increase might actually have a chance affecting the free 
surfer processes :)


Best
        Sebastian



On Dec 4, 2012, at 09:41 , Negar Memarian wrote:

> Hello,
> In the VM setting, I increased the RAM to 8 GB (my computers' maximum) and 
> increased number of working CPUs to 4. Unfortunately the crash still happens 
> in the "EM Registration" stage with a similar error, i.e.,
> gcaAllocMax: node dims 64 64 64
> gcaAllocMax: prior dims 128 128 128
> gcaAllocMax: max_labels 0
> Cannot allocate memory
> Linux VMprivate 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 
> x86_64 x86_64 GNU/Linux
> recon-all -s testimport exited with ERRORS at Mon Dec 3 16:38:39 PST 2012
> I have attached a screenshots of the result of "top" command,  as well as the 
> VM's system monitor graphs during the recon-all process before it crashed. I 
> have also attached the recon-all.log file.
> Would you kindly bring this question to the attention of Nick and PPJ? I 
> really need to get this to work.
> 
> Best regards,
> Negar
> 
> On Mon, Dec 3, 2012 at 5:42 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> 
> wrote:
> Hi Negar
> 
> perhaps Nick or PPJ can comment on how much a virtual box needs? In any case, 
> try increasing the ram and see what happens as the error message is pretty 
> clear. Also, if you can run "top" or something similar (/usr/bin/free) to see 
> how memory is actually available on the system that would help
> 
> cheers
> Bruce
> 
> On Sat, 1 Dec 2012, Negar Memarian wrote:
> 
> Thank you for your reply, Bruce. I'm running FreeSurfer using a VMWare
> virtual machine on Windows 7. I've set the settings of the VM to use 2 CPUs
> and 6GB ram. Here is the specifications of my computer hardware:
> OS: Windows 7 professional
> Processor: Intel Core i7-3770 CPU @ 3.40 GHz
> RAM: 8 GB
> System type: 64 bit
> 
> Please let me know if you need any other info. Many thanks for your help.
> -Negar
>  
> 
> On Sat, Dec 1, 2012 at 11:52 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>       can you check to see how much you actually have free? You are
>       definitely running out of memory, so something else is using it.
>       What is your hardware/software environment?
> 
>       On Sat, 1 Dec 2012, Negar Memarian wrote:
> 
>             No, I tried running just one recon and I only have
>             one xterm window open.
>             Anything I can do to fix this? 
> 
> 
> 
>             On Sat, Dec 1, 2012 at 11:11 AM, Bruce Fischl
>             <fis...@nmr.mgh.harvard.edu>
>             wrote:
>                   6G should be plenty. Do you have anything else
>             running? Maybe
>                   another recon at the same time?
>                   On Fri, 30 Nov 2012, Negar Memarian wrote:
> 
>                         Hi Bruce,
>                         I have 8 GB ram and have assigned 6GB of
>             it to
>                         FreeSurfer. Shall I increase
>                         it to 8? Would that be enough or still
>             too low?
> 
>                         Thank you,
>                         Negar
> 
> 
>                         On Fri, Nov 30, 2012 at 7:31 PM, Bruce
>             Fischl
>                         <fis...@nmr.mgh.harvard.edu>
>                         wrote:
>                               Look like it is running out of
>             memory. How
>                         much ram do you have
>                               on that machine?
>                               Bruce
> 
> 
> 
>                               On Nov 30, 2012, at 9:29 PM, Negar
>             Memarian
>                               <negar.memar...@utoronto.ca>
>             wrote:
> 
>                               > Hello,
>                               >
>                               > I ran recon-all -all on my
>             subject. The
>                         process ended after
>                               several minutes with this message
>             at the end:
>                               > recon-all -s 350_FS exited with
>             ERRORS at
>                         Fri Nov 30 17:57:59
>                               PST 2012
>                               >
>                               > I tried loading the pial and
>             white surfaces
>                         for editing using
>                               this command:
>                               > tkmedit 350_FS brainmask.mgz
>             rh.white
>                         -aux-surface lh.white
>                               >
>                               > but looks like these surfaces do
>             not exist
>                         (since the
>                               recon-all exited prematurely).
>             When I check
>                         the recon-all.log
>                               file I do not see any errors
>             except a few
>                         MCSRCH errors. So I
>                               cannot understand what exactly
>             went wrong in
>                         the recon-all. I've
>                               attached the recon-all log file.
>             Can someone
>                         please tell me what
>                               the problem is and how I can fix
>             it?
>                               >
>                               > Many thanks,
>                               > Negar
>                               > p.s. I tried on more than one
>             subject and I
>                         still face the
>                               same issue.
>                               >
>                               >
>                               > Negar Memarian, MASc, PhD
>                               > NSERC Postdoctoral Fellow
>                               > Department of Neurology
>                               > David Geffen School of Medicine
>             at UCLA
>                               >
>                               > <recon-all.log>
>                               >
>                        
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> 
> 
> 
> 
> 
> <screeshot-top.JPG><recon-all.log>_______________________________________________
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-- 
Sebastian Moeller

telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
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