Hi Bruce,
Any luck with what went wrong? Thanks, Sneha ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@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-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > > <fis...@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 > > > > > > > > > > > > > > > > > >
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