Hi Bruce,

Thanks to your advice, I was able to generate a mgh file using mri_vol2surf, and thus map the texture onto both the inflated and the flattened surfaces.

I wonder whether it is possible to reversely map the vertices on the vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to the voxels in the volumetric file (mgz file), i.e. find the xyz coordinate of each vertex in the frame of reference of the volumetric file (mgz file) used to generate the vectorized surface.

Also, I’ve noticed that the number of the columns in the texture mapping file (i.e. ‘lh.sig.mgh’, the output of mri_vol2surf command), is equal to the number of the vertices on the vectorized surface. I assume that the texture mapping file and the vectorized surface has a one-to-one vertex/column correspondence. If so, I wonder how the texture intensity of each vertex is stored in the texture mapping file and eventually mapped onto the vectorized surface.

Thanks,

Younghoon Kim

--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
----------------------------------------------
younghoon.h.kim@gmail.com
aktivhoon@kaist.ac.kr

On July 26, 2016 at 5:51:01 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:

sure, you can do that with mri_vol2surf. Basically the initial surface
and the final (inflated) surface have the same number of vertices, so the
vertex identity is preserved and mri_vol2surf samples values from the
volume onto the surface which can then be displayed on any surface
configuration (like inflated)

On Tue, 26 Jul 2016, Younghoon Kim wrote:

> 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.kim@gmail.com
> aktivhoon@kaist.ac.kr
>
> On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fischl@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.kim@gmail.com
> > aktivhoon@kaist.ac.kr
> >
> >
> > On July 21, 2016 at 10:35:18 AM, Bruce Fischl
> (fischl@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.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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