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

[Steve Lancey]

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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> ----------------------
> 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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