[Insight-users] Using the meshing classes in ITK

Thu Dec 3 20:36:13 EST 2009

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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>
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>
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>
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