[Insight-users] Using the meshing classes in ITK

[Andriy Fedorov]

Anja,

Here's a package that you might find helpful:

http://iso2mesh.sourceforge.net/

I personally never used it, but I did have good experience with Tetgen
and CGAL for the tasks similar to what you want to accomplish. From
the first look, iso2mesh appears to be a wrapper around several lower
level meshing tools (including Tetgen and some algorithms from CGAL).

You can use CGAL+Tetgen directly to construct a tetrahedral mesh from
segmentation, but this will require some time to understand formats,
parameters, and write some extra code. It looks like iso2mesh does
this transparently from the user, but I have not tried it myself to
confirm this.

If you do use this iso2mesh tool, please update the list with your experience.

Andriy Fedorov




> Date: Wed, 2 Dec 2009 18:46:25 -0500
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Using the meshing classes in ITK
> To: Anja Ende <anja.ende at googlemail.com>
> Cc: insight-users at itk.org
> Message-ID:
>        <f7abd23c0912021546y796561f2y93d4dedc095761af at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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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