Negar, This appears to be a strange problem. From the recon-all.log file, the important error is this one:
GCAread(/usr/local/freesurfer/average/RB_all_2008-03-26.gca): couldn't expand gcs to 1114693712 which means it failed to alloc the 1.2GB needed to load the atlas. but given that earlier in the log it says that there is 6974628 (6GB) free, it would seem that there is plenty of memory. i would try two things: - first try running recon-all -s bert -all, where you can copy the subject 'bert' from freesurfer/subjects, to see if it fails as well. - then per sebastians suggestion, download and install the 64b centos freesurfer build. you can do that within your vm. your existing 32b should work so i am doubtful that 64b will work, but at the moment i'm at a loss as to the problem. nick On Tue, 2012-12-04 at 12:35 -0800, Sebastian Moeller wrote: > 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.moell...@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 <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 > > > > > > 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
