Hi Negar,
On Dec 4, 2012, at 12:19 , Negar Memarian wrote:
Hi Sebastian,
Thank you for your reply. The virtual machine that I'm using was built by a friend who also uses FreeSurfer and I copied it entirely onto my computer (a huge folder, 263GB). Freesufer works just fine for him. So whatever version of Freesurfer he's using, it's working for him and I'm basically replicating exactly what he has on his computer and yet not able to complete the recon-all -all process. Any ideas?
Sorry, no real idea. But can you have your friend run your subjects under his installation (I assume you are not trying to recon subjects that your friend already suddessfully reconned)? I assume that it will also fail, as the amount of memory required of some steps (not necessarily of the one that fails for you, I do not really know the free surfer code base well enough (read at all :) ) to judge). So if it also fails for the same subject for him, then I would really recommend to install the 64 bit free surfer version (can be installed in parallel so you can switch between the two) and these that. Testing the 64bit version seems like a no brainer to me, as your failure just takes around 3 minutes to materialize… But I am already at the end of my knowledge here…
Thank you, Negar
On Tue, Dec 4, 2012 at 10:57 AM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: 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
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