Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Sebastian Moeller
Hi Negar, I guess this is where I have to leave the issue to Nick and Bruce as I am way out of my league here :). It would have been nice if switching to 64bit free surfer would have fixed the issue. One observation though, it looks like you are using the bert subject that was distributed with

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Bruce Fischl
Hi Negar why don't you upload your dataset (the whole subject directory) and we'll see if there is anything strange about it. Have you ever completed a recon successfully? Have you tried running it on Bert's excellent brain? Bruce On Tue, 4 Dec 2012, Negar Memarian wrote: Hi Nick, Sebasti

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Sebastian Moeller
Hi Nick, On Dec 4, 2012, at 14:41 , Nick Schmansky wrote: > 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 i

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Nick Schmansky
Negar, Another option is to try another vm. While we have our own vm w/freesurfer Ubuntu instance, people have had success with installing the FSL VM, which is built with Centos, and then within that download and install the 64b freesurfer instance. Although the background images in your attache

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Nick Schmansky
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 i

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Sebastian Moeller
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.

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Negar Memarian
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

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-04 Thread Sebastian Moeller
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 memo

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-03 Thread Bruce Fischl
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 w

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-01 Thread Negar Memarian
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 Syste

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-01 Thread Bruce Fischl
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. Anyt

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-01 Thread Negar Memarian
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 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 w

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-01 Thread Bruce Fischl
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, > Ne

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-11-30 Thread Negar Memarian
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 wrote: > Look like it is running out of memory. How much ram do you have on that > machine? > Bruc

Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-11-30 Thread Bruce Fischl
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 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 wit