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> > > > > _______________________________________________ > > 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. -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer