Thank you Dough, yes I believe so, we have matlab and spm installed as well.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <greve@nmr.mgh.harvard.edu>
Sent: Tuesday, January 24, 2017 5:00:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
 
The -spm will work well, but it does require matlab (and spm). Note that
in version 6 we use mri_coreg which is our implementation of spmreg.


On 01/24/2017 02:15 PM, Hoopes, Andrew wrote:
>
> 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.mgzas 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-headerI independentlytried bbregister with
> bbr-init-fsl and bbr-init-spm. bbregister only worked with
> bbr-init-spmresulting innon-empty and properly registered
> FLAIR.prenorm.mgzand non-emptyFLAIR.mgz volume in the mri_normalize
> step. I tried this with only one case, so not sure if it will be
> successfulfor others as well.
>
>
> Do you suggest I run them with bbr-init-spmor registering with
> FLAIRraw to the origas you suggested. Ifbbr-init-spmis fine then
> withwhich step of recon should I run? I tried running it with
> autorecon3step with bbr-init-spmand FLAIRpialflags, but it did not
> overwrite FLAIR.prenorm.mgz and FLAIR.mgzvolumes.
>
>
> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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