Hi Bruce,


Total is 231111108 kB from /proc/meminfo and flair vozel size is 1.0000, 0.9766, 0.9766.


I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run recon-all -autorecon3 with -bbr-init-header flag.


Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Wednesday, January 18, 2017 11:09:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
 
Hi Sneha

how much RAM do you have in your machine? And what is the resolution of
your data?

cheers
Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:

>
> Hi all,
>
>
> I have successfully ran recon-all on my subjects with multiple T1s. We want
> to use flair to refine pial surfaces as for all the subjects pial surfaces
> are messy and will demand lots of control point edits.
>
>  
>
> After successfully running entire recon-all stream I am running following
> command to incorporate flair:
>
>
> recon-all -autorecon3 \
>         -s SUBJ \
>         -bbr-init-header \
>         -FLAIRpial \
>         -bigventricles \
>         -openmp 12 \
>         -qcache
>
> When I run above command recon-all exits while implementing
> mris_make_surfaces with an error "Cannot allocate memory"
>
> Can someone guide what is happening? Is it that there are large topological
> error or bbr-init-header flag will only run if I run recon-all from
> autorecon1 to autorecon3 stage?
>
> Thanks,
>
> Sneha
>
>
>
>