is Brain_FS.mgz a segmented volume? How much memory do you have on that
machine?

On Wed, 20 Jul 2016, Younghoon Kim wrote:

> Hi Bruce,
>
> I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a
> surface, but received an error message as below:
>
> changing type of input volume to 8 bits/voxel...
> $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
> Cannot calloc()
>
> Would this be because my input data is not compatible with the mri_tessellate
> command?
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> ----------------------------------------------
> younghoon.h.kim@gmail.com
> aktivhoon@kaist.ac.kr
>
> On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
>
> If you have a segmented volume, you can use mri_tessellate to create the
> surface, then introduce the cut(s) and run mris_flatten -1 on the resulting
> patch. You can check out our wiki
>
> http://surfer.nmr.mgh.harvard.edu/fswiki
>
> which has info on this process, although the flattening isn't terribly well
> documented. You need the -1 flag to tell it to only use that one surface
> that you are giving it, and not to assume that the entire FS directory
> structure exists.
>
> cheers
> Bruce
>
>
> On Wed, 20 Jul 2016, Younghoon Kim wrote:
>
> > Hi Bruce,
> >
> > Great! I’m not an expert in FreeSurfer, so can you give me some advice how
> to
> > generate a surface of our volumetric data and flatten it?
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > ----------------------------------------------
> > younghoon.h.kim@gmail.com
> > aktivhoon@kaist.ac.kr
> >
> > On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
> wrote:
> >
> > HI Younghoon
> >
> > I guess that could work. You will need to introduce at least one cut if not
> > more if you surface has substantial Gaussian curvature
> >
> > cheers
> > Bruce
> >
> >
> > On Wed,
> > 20 Jul 2016, Younghoon Kim wrote:
> >
> > > Hi Bruce,
> > >
> > > We are only interested in the surface image of the volumetric data.
> > >
> > > For flattening, we do not care about the interior of the volume, so we
> > would like
> > > to remove the volume data inside.
> > >
> > > So what we want is to peel off the surface from the segmented brain area
> > and
> > > flatten that surface.
> > >
> > > Thanks,
> > >
> > > Younghoon Kim
> > >
> > > --
> > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > OMICS Lab
> > > Wellman Center, Massachusetts General Hospital
> > > Bouma’s Lab
> > > ----------------------------------------------
> > > younghoon.h.kim@gmail.com
> > > aktivhoon@kaist.ac.kr
> > >
> > > On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
> > wrote:
> > >
> > > Hi Younghoon
> > >
> > > what structure are you talking about? In general it doesn't make sense to
> > > flatten volumetric structures. We flatten the cortex, which is a folded
> > > 2D sheet. What would you do with the interior of the volume?
> > >
> > > cheers
> > > Bruce
> > > On Wed, 20 Jul
> > > 2016, Younghoon Kim wrote:
> > >
> > > > Hello,
> > > >
> > > > We have a volumetric data (mgz file) of a segmented brain region. We
> want
> > > to detect
> > > > the surface of this segmented brain volume (i.e. deep brain region) and
> > > flatten it
> > > > into a 2D image with its original surface texture.
> > > >
> > > > We’ve noticed that Freesurfer supports an algorithm to flatten
> volumetric
> > > data. We
> > > > wonder if this could be adapted to our data set. Can anyone offer some
> > > advice on
> > > > how to apply FreeSurfer to this more generic task?
> > > >
> > > > Thanks,
> > > >
> > > > Younghoon Kim
> > > >
> > > > --
> > > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > > OMICS Lab
> > > > Wellman Center, Massachusetts General Hospital
> > > > Bouma’s Lab
> > > > ----------------------------------------------
> > > > younghoon.h.kim@gmail.com
> > > > aktivhoon@kaist.ac.kr
> > > >
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