[Insight-users] Re: [Insight-developers] Mesh from binary mask options

[Luis Ibanez]

Hi Richard,

Yes, using your binary mask for initializing a LevelSet and then
let it run for several iterations is also an option.

Actually, this is what the AntiAlias filter does, although it adds
the constrain of not letting the front move more than one pixel
away from its original position.

You could use any of the LevelSet classes in ITK (except FastMarching)
and then simply pass the output level set to VTK by converting it to
a vtkImageData class. Once inside VTK you use the vtkContourFilter
and as iso-value, the *same* value that defined the zero-set in the
ITK LevelSet filter.

Note that it is better to transfer the LevelSet image to VTK and then
use the VTK contour filter than trying to extract a contour in ITK as
an ITK Mesh and then convert that mesh to a vtkPolyData.


You may want to look at the code of ITKSnap:

              InsightApplications/SNAP




   Regards,


      Luis



-------------------
Richard Beare wrote:
> Hi,
> 
> I've done some experiments using the anti aliasing filter, but
> experience similar problems.
> 
> I'm starting to suspect that the way to go may be to initialize a
> level set with my original segmentation image and let it evolve on a a
> gradient image and transfer the mesh resulting from the level set to
> vtk. Is that sort of thing possible?
> 
> On 8/17/06, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
>>
>> Hi Richard,
>>
>> Have you tried smoothing the ITK binary image mask
>> before passing it to a vtkImageData ?
>>
>> You may want to try the itkAntiAliasImageFilter.
>> It will smooth the image and still guarantee that
>> the iso-contours are in the same pixels as they
>> were for the Binary Mask.
>>
>> By passing a smoother isocontour you may have
>> better luck when decimating the surface.
>>
>>
>>     Regards,
>>
>>
>>        Luis
>>
>>
>> -----------------------
>> Richard Beare wrote:
>> > Hi,
>> >
>> > I've been playing with FeatureEdgeSmoothing in
>> > vtkWindowedSincPolyDataFilter and setting a feature angle of around
>> > 140 degrees, but still tend to see the thin filaments I mentioned get
>> > broken. Now that I'm using the contour filter they are unbroken prior
>> > to smoothing. Is there any way to smooth while preserving topology?
>> >
>> > Thanks
>> >
>> > On 8/16/06, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>> >
>> >>
>> >> Hi Richard,
>> >>
>> >> If you are already combining ITK and VTK, it will be much better
>> >> to convert your ITK binary mask to a vtkImageData and then use
>> >> the vtkContourFilter on it.
>> >>
>> >>
>> >> The vtkContourFilter is much better than the
>> >> itk::BinaryMask3DMeshSource.
>> >>
>> >>
>> >> You will find examples on how to convert itkImage to vtkImageData
>> >> in the InsightApplications/Auxiliary/vtk directory.
>> >>
>> >>
>> >> for example:
>> >>
>> >>       itkReadITKImage3DSegmentShowVTK.cxx
>> >>       itkReadITKImageSegmentShowVTK.cxx
>> >>       itkReadITKImageShowSplineVTK.cxx
>> >>       itkReadITKImageShowVTK.cxx
>> >>
>> >>
>> >>
>> >>     Regards,
>> >>
>> >>
>> >>
>> >>        Luis
>> >>
>> >>
>> >> -----------------------
>> >> Richard Beare wrote:
>> >> > Hi everyone,
>> >> >
>> >> > I'm using itk::BinaryMask3DMeshSource to create a mesh from a mask
>> >> > I've generated. I translate the resulting mesh to an stl file via
>> >> > itkMeshTovtkPolyData and vtkSTLWriter (and optionally
>> >> > vtkWindowedSincPolyDataFilter). Some of the masks I'm producing have
>> >> > quite fine structure - for example 1 voxel thick filaments. 
>> Naturally
>> >> > the mesh produced by the marching cubes algorithm does not include
>> >> > this sort of structure - the interpretation of such structures is
>> >> > application dependent. In my case I would like to have the filaments
>> >> > represented in the mesh as tubes. One hack that would achieve 
>> this is
>> >> > to resample the mask so that the filaments are no longer one pixel
>> >> > thick and apply the marching cubes as before. However I was 
>> wondering
>> >> > if there is any other approach. I'm not tied to stl, I just need
>> >> > something that can be imported by typical cad packages. In addition,
>> >> > if anyone can recommend a way of producing a nurbs based
>> >> > representation from (or instead of) the triangulation, I'd like to
>> >> > hear about it.
>> >> >
>> >> > Thanks.
>> >> > _______________________________________________
>> >> > Insight-developers mailing list
>> >> > Insight-developers at itk.org
>> >> > http://www.itk.org/mailman/listinfo/insight-developers
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>> >
>>
>>
>>
> 
>