Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented
brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is needed
for further steps in my project.
I am considering to project the texture of the segmented brain area (the
pixel intensity on the surface of the volumetric data) to the generated
surface (vectorized surface). I wonder whether this can be done in a similar
way to the way you project fMRI signal to the 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....@gmail.com
aktivh...@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
and 255 is the label that you want to cover? 16G may not be enough. Do
you
have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon
Kim wrote:
> Hi Bruce,
>
> Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using
different imaging methods)
>
> Our machine has 16GB RAM.
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> ----------------------------------------------
> younghoon.h....@gmail.com
> aktivh...@kaist.ac.kr
>
>
> On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fis...@nmr.mgh.harvard.edu) wrote:
>
> 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....@gmail.com
> > aktivh...@kaist.ac.kr
> >
> > On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fis...@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....@gmail.com
> > > aktivh...@kaist.ac.kr
> > >
> > > On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fis...@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....@gmail.com
> > > > aktivh...@kaist.ac.kr
> > > >
> > > > On July 20, 2016 at 5:00:55 PM, Bruce Fischl
(fis...@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....@gmail.com
> > > > > aktivh...@kaist.ac.kr
> > > > >
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