hmmm, can you send us the recon-all.log file?

On Wed, 18 Jan 2017, Sneha Pandya wrote:

>
> 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
> >
> >
> >
> >
>
>