[Insight-users] Deformable registration using FEM: Visualize Mesh

[Vincent Magnotta]

Just to follow-up to Luis's e-mail.

There is another solution to the mesh visualization question. What we have
done in some of our code is to have a parallel copy of the mesh in VTK that
we update the point locations based on the results of the FE analysis. This
can then be written to disk and visualized and animated in Paraview.

The software that was mentioned for mesh generation (IA-FEMesh) is both a 3D
Slicer module and has a stand-alone version
(http://www.ccad.uiowa.edu/mimx). Given a surface, you can generate a
hexahedral mesh and assign material properties. The mesh can be saved in VTK
format where the material properties are stored as Cell data. You will need
to write some code to create an ITK FE mesh from the resulting VTK mesh. I
have an example if that will be helpful. The ITK FEM framework is an area
where some refactoring is needed. Hopefully you will some work in this area
with the push towards ITK4.

Vince


On 2/23/10 4:23 PM, "Luis Ibanez" <luis.ibanez at kitware.com> wrote:

> Hi Steve,
> 
> Option (A)
> 
> The original FEM code in ITK has a compile flag:
> 
>           FEM_BUILD_VISUALIZATION
> 
> but, given that Visualization was not in the scope of
> ITK, this code has probably never been exercised.    :-(
> 
> 
> Option (B)
> 
> You could use the filters that overlap a grid on an
> image, and resample that grid image through the
> deformation field computed by the FEM registration
> method.
> 
> See
>              Insight/Code/Review/
>                            itkGridImageSource.h
> 
> and its explanation in the Insight Journal paper
> 
>             "Gridding Graphic Graticules"
>             Tustison N., Avants B., Gee J.
>             University of Pennsylvania
>             http://hdl.handle.net/1926/475
> http://www.insight-journal.org/browse/publication/140
> 
> 
> -----
> 
> Regarding the process of creating a customized
> Mesh:
> 
>         We don't have such functionality in ITK.
> 
> Mesh Generation is outside of the scope of ITK.
> 
> You will find very useful to look at:
> 
> http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Me
> sh_Development
> 
> as a possible solution.
> 
> This is an Open Source application based
> on ITK and VTK
> 
> 
> 
>      Regards,
> 
> 
>                Luis
> 
> 
> 
> -------------------------------------------------------
> On Mon, Feb 22, 2010 at 9:52 PM, Steve Lancey <steve.lancey at gmail.com> wrote:
>> Hi,
>> 
>> I have two questions:
>> 
>> 1) I would like to store the generated mesh after every iteration of the
>> energy minimization procedure and visualize them later (as a binary images
>> or paths).
>> What is the best way to achieve this?
>> 
>> 2) What is the best tool to create a mesh manually, including the assignment
>> of mesh element properties?
>> 
>> Thanks for taking your time,
>> 
>> Steve Lancey
>> 
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----------------------
Associate Professor
Department of Radiology
0453-D JCP
200 Hawkins Drive
Iowa City, IA 52242
E-mail: vincent-magnotta at uiowa.edu
Phone: 319-356-8255 Fax: 319-353-6275
Website: http://www.radiology.uiowa.edu