Ah great! If the registration is accurate with bbr-init-spm, I suggest just using that. I would only use the mri_robust_register technique if none of the bbr initialization options produce a precise alignment. To overwrite the FLAIR volumes, I'm pretty sure including the "-clean-FLAIR" flag in your autorecon3 command will do the job.


best,

Andrew

From: Sneha Pandya <snp2003@med.cornell.edu>
Sent: Tuesday, January 24, 2017 12:49:31 PM
To: Hoopes, Andrew; Freesurfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
 

Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgz as their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).


In addition to bbr-init-header I independently tried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spm resulting in non-empty and properly registered FLAIR.prenorm.mgz and non-empty FLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successful for others as well.


Do you suggest I run them with bbr-init-spm or registering with FLAIRraw to the orig as you suggested. If bbr-init-spm is fine then with which step of recon should I run? I tried running it with autorecon3 step with bbr-init-spm and FLAIRpial flags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgz volumes.


Thanks,
Sneha
From: Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
Sent: Tuesday, January 24, 2017 12:20:03 PM
To: Freesurfer support list; Sneha Pandya
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
 

Hi Sneha,

I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:

cd 1_S_5002_snp_bbr-init-header/mri/orig
mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit
cp FLAIRraw.mgz FLAIRcopy.mgz
mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample

This should do the trick.

best,
Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2003@med.cornell.edu>
Sent: Thursday, January 19, 2017 1:42:06 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
 

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

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