[Insight-users] Using the meshing classes in ITK

[Anja Ende]

Thank you all for your reply. I will try the iso2Mesh tool and will
let the list know about my experience.

Cheers,
Anja

2009/12/3 Andriy Fedorov <fedorov at bwh.harvard.edu>:
> 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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>



-- 
Cheers,

Anja