Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Wednesday, January 18, 2017 2:43:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
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 1:58:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
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 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header 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