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 fischl@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 fischl@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 <fischl@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 <fischl@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.memarian@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> > _______________________________________________ > 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.<screeshot-top.JPG><recon-all.log>_______________________________________________ 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.