[Insight-users] Using the meshing classes in ITK

Anja Ende anja.ende at googlemail.com
Sat Dec 5 18:42:21 EST 2009 

Many thanks Stefan!

2009/12/4 Stefan Dänzer <stefan.daenzer at gmail.com>:
> Anja,
>
> there's also another tool you might want to have a look at for generating
> tetrahedral meshes. It's called "Voxelizer" by Dan Morris, you can get it
> here: http://techhouse.brown.edu/~dmorris/projects/voxelizer/
>
> I have used it in the past to generate volumetric meshes from a surface
> representation in a virtual surgical training simulator a while ago.
>
> Good luck with your work!
>
> Stefan
>
> On Thu, Dec 3, 2009 at 12:45 PM, Anja Ende <anja.ende at googlemail.com> wrote:
>>
>> 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
>> _____________________________________
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>>
>> Visit other Kitware open-source projects at
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>>
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>>
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>
>
>
> --
> --
> Stefan Daenzer
> Körnerplatz 8
> 04107 Leipzig
>
> Tel.: +49-176-61157550
>
> "Work like you don't need the money, love like you've never been hurt and
> dance like no one is watching." - Randall G Leighton
>



-- 
Cheers,

Anja

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