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

Mon Mar 8 09:10:56 EST 2010

Steve,

Attached are two classes that should help. They do not carry along the
material property information. This would need to be added.

Vince

On 3/7/10 3:55 PM, "Steve Lancey" <steve.lancey at gmail.com> wrote:

> Hi Vincent,
> 
> This is great news, just downloaded the software. It would be great sending me
> the code snippet for converting the mesh.
> What code do you use for surface extraction?
> 
> Thx,
> 
> S.
> 
> On Tue, Feb 23, 2010 at 10:39 PM, Vincent Magnotta
> <vincent-magnotta at uiowa.edu> wrote:
>> 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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>>>> >>
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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
>> 
>> 
>> 
> 
> 

----------------------
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

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