[Insight-users] Using the meshing classes in ITK

[Luis Ibanez]

Hi  Anja,

                  Welcome to ITK !

Your question is a very interesting one.


And to put it shortly:

         It is one for which we don't have
         a full answer involving only ITK methods.


There are two major pieces to what you are
trying to do:

1)  Segmenting brain structures from MR  and CT brain data.

2)  Generating tetrahedral meshes from the segmented
     regions



For (1), ITK provides a very rich set of methods.


For (2), you will have to use additional tools.


Regarding (1), the type of segmentation methods that you
need to use is closely related to the specific brain structure
that you want to segment.

Popular methods are:

* Region growing
* Level Sets
* Statistical Classification
* Atlas-based segmentation

and combinations of them, for example

* EM segmentation.

You will find an introduction to (some of the)
segmentation methods in ITK, in the
Software Guide:

  http://www.itk.org/ItkSoftwareGuide.pdf


You will also find a good deal of Brain segmentation
tools at NAMIC:
http://www.na-mic.org/Wiki/index.php/Main_Page

and

NITRC:
http://www.nitrc.org/


Many of them, based on ITK.



Regarding the tetrahedral mesh generation:
ITK itself does not provide that functionality.

The tool that you should try is:
http://www.ccad.uiowa.edu/mimx/IA-FEMesh/

(which is also used by several groups at NAMIC):
http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development


This tool needs as input a surface.
(a 2D manifold embedded in a 3D space)

You can generate such surface by taking the
segmentation (typically a binary image) of the
brain structures of your interests and extracting
its Iso-surface with VTK (typically with the
vtkContourFilter) or with a ready-to-use tool
like ParaView http://www.paraview.org).
(which is based on VTK).



     Please take a look at these resources
     and let us know if you have further
     questions,


            Thanks


                  Luis



-------------------------------------------------------------------------------------
On Wed, Dec 2, 2009 at 6:56 AM, Anja Ende <anja.ende at googlemail.com> wrote:
> Hello everyone,
>
> This is more of a general question. I would like to know more about
> generating meshes from MR and CT data. So, I have a brain image and I
> would like to generate a tetrahedral based mesh from it and then use
> it further for some FEM processing. I am a newbie to this field and
> would like to ask a couple of questions and would be very grateful if
> someone can take the time to answer them:
>
> - What pre-processing do I need to do to the itk image so that I can
> feed it to a mesh generator? Would I first need to segment the bit
> that I am interested in? So, would I need to segment the background
> out of the image.
> - I am guessing the mesh generators would need some point set as their
> input. How could I generate a point set from an itk image?
>
> I am quite new to this area and am a bit lost as to how to start.
> Would really appreciate your help.
>
> Cheers,
>
> Anja
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