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<TITLE>Re: [Insight-users] Deformable registration using FEM: Visualize Mesh</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Steve,<BR>
<BR>
Attached are two classes that should help. They do not carry along the material property information. This would need to be added.<BR>
<BR>
Vince<BR>
<BR>
<BR>
<BR>
On 3/7/10 3:55 PM, "Steve Lancey" <<a href="steve.lancey@gmail.com">steve.lancey@gmail.com</a>> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi Vincent,<BR>
<BR>
This is great news, just downloaded the software. It would be great sending me the code snippet for converting the mesh.<BR>
What code do you use for surface extraction?<BR>
<BR>
Thx,<BR>
<BR>
S.<BR>
<BR>
On Tue, Feb 23, 2010 at 10:39 PM, Vincent Magnotta <<a href="vincent-magnotta@uiowa.edu">vincent-magnotta@uiowa.edu</a>> wrote:<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Just to follow-up to Luis's e-mail.<BR>
<BR>
There is another solution to the mesh visualization question. What we have<BR>
done in some of our code is to have a parallel copy of the mesh in VTK that<BR>
we update the point locations based on the results of the FE analysis. This<BR>
can then be written to disk and visualized and animated in Paraview.<BR>
<BR>
The software that was mentioned for mesh generation (IA-FEMesh) is both a 3D<BR>
Slicer module and has a stand-alone version<BR>
(<a href="http://www.ccad.uiowa.edu/mimx">http://www.ccad.uiowa.edu/mimx</a>). Given a surface, you can generate a<BR>
hexahedral mesh and assign material properties. The mesh can be saved in VTK<BR>
format where the material properties are stored as Cell data. You will need<BR>
to write some code to create an ITK FE mesh from the resulting VTK mesh. I<BR>
have an example if that will be helpful. The ITK FEM framework is an area<BR>
where some refactoring is needed. Hopefully you will some work in this area<BR>
with the push towards ITK4.<BR>
<BR>
Vince<BR>
<BR>
<BR>
On 2/23/10 4:23 PM, "Luis Ibanez" <<a href="luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>> wrote:<BR>
<BR>
> Hi Steve,<BR>
><BR>
> Option (A)<BR>
><BR>
> The original FEM code in ITK has a compile flag:<BR>
><BR>
> FEM_BUILD_VISUALIZATION<BR>
><BR>
> but, given that Visualization was not in the scope of<BR>
> ITK, this code has probably never been exercised. :-(<BR>
><BR>
><BR>
> Option (B)<BR>
><BR>
> You could use the filters that overlap a grid on an<BR>
> image, and resample that grid image through the<BR>
> deformation field computed by the FEM registration<BR>
> method.<BR>
><BR>
> See<BR>
> Insight/Code/Review/<BR>
> itkGridImageSource.h<BR>
><BR>
> and its explanation in the Insight Journal paper<BR>
><BR>
> "Gridding Graphic Graticules"<BR>
> Tustison N., Avants B., Gee J.<BR>
> University of Pennsylvania<BR>
> <a href="http://hdl.handle.net/1926/475">http://hdl.handle.net/1926/475</a><BR>
> <a href="http://www.insight-journal.org/browse/publication/140">http://www.insight-journal.org/browse/publication/140</a><BR>
><BR>
><BR>
> -----<BR>
><BR>
> Regarding the process of creating a customized<BR>
> Mesh:<BR>
><BR>
> We don't have such functionality in ITK.<BR>
><BR>
> Mesh Generation is outside of the scope of ITK.<BR>
><BR>
> You will find very useful to look at:<BR>
><BR>
> <a href="http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Me">http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Me</a><BR>
> sh_Development<BR>
><BR>
> as a possible solution.<BR>
><BR>
> This is an Open Source application based<BR>
> on ITK and VTK<BR>
><BR>
><BR>
><BR>
> Regards,<BR>
><BR>
><BR>
> Luis<BR>
><BR>
><BR>
><BR>
> -------------------------------------------------------<BR>
> On Mon, Feb 22, 2010 at 9:52 PM, Steve Lancey <<a href="steve.lancey@gmail.com">steve.lancey@gmail.com</a>> wrote:<BR>
>> Hi,<BR>
>><BR>
>> I have two questions:<BR>
>><BR>
>> 1) I would like to store the generated mesh after every iteration of the<BR>
>> energy minimization procedure and visualize them later (as a binary images<BR>
>> or paths).<BR>
>> What is the best way to achieve this?<BR>
>><BR>
>> 2) What is the best tool to create a mesh manually, including the assignment<BR>
>> of mesh element properties?<BR>
>><BR>
>> Thanks for taking your time,<BR>
>><BR>
>> Steve Lancey<BR>
>><BR>
>> _____________________________________<BR>
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><BR>
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<BR>
----------------------<BR>
Associate Professor<BR>
Department of Radiology<BR>
0453-D JCP<BR>
200 Hawkins Drive<BR>
Iowa City, IA 52242<BR>
E-mail: <a href="vincent-magnotta@uiowa.edu">vincent-magnotta@uiowa.edu</a><BR>
Phone: 319-356-8255 Fax: 319-353-6275<BR>
Website: <a href="http://www.radiology.uiowa.edu">http://www.radiology.uiowa.edu</a><BR>
<BR>
<BR>
<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
----------------------<BR>
Associate Professor<BR>
Department of Radiology<BR>
0453-D JCP<BR>
200 Hawkins Drive<BR>
Iowa City, IA 52242<BR>
E-mail: <a href="vincent-magnotta@uiowa.edu">vincent-magnotta@uiowa.edu</a><BR>
Phone: 319-356-8255 Fax: 319-353-6275<BR>
Website: <a href="http://www.radiology.uiowa.edu">http://www.radiology.uiowa.edu</a><BR>
<BR>
<BR>
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