Mia,
also i noticed this at the top of the log:
total used free
Mem: 37010736 19490372 17520364
-/+ buffers/cache: 10784236 26226500
Swap: 8393952 150528 8243424
it shows that just 1.7GB is available for the recon to run, which is
below what we recommend. recon-all usually needs at least 2GB.
after inspecting for defects like doug suggests, you could try stopping
other apps that are consuming mem (or just reboot which will ensure
maximal free memory) and then run recon-all -make all
Nick
On Wed, 2013-01-23 at 13:23 -0500, Douglas N Greve wrote:
> Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge
> defect (like the entire cerebellum is attached). You can run
>
> tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix
>
> Note that you will get a few error messages when loading the orig.nofix
> surface. These can be ignored
>
> doug
>
> On 01/23/2013 12:19 PM, Borzello, Mia wrote:
> > Hey Freesurfers,
> >
> > I received a "Cannot allocate memory" error while running a recon
> > overnight. I think there should be enough space on the machine to store the
> > data so I'm suspicious that it's a different memory problem.
> > I attached the recon-all.log file.
> >
> > Thanks for your help!
> > m
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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