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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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