[Insight-users] itk + vtk segmentation questions

[Luis Ibanez]

Hi Jacob,


1) There are multiple methods for constructing 3D data
    sets from a set of slices.

    In the case of the Visible Human, the simplest
    thing to do is to write a MetaImage header file.

    You will find instructions on how to do this in
    the Data link

           http://www.itk.org/HTML/Data.htm

    You will find one for the Visible Woman dataset in
    the ftp data repository:

ftp://public.kitware.com/pub/itk/Data/VisibleWomanHead/RawRGB/
ftp://public.kitware.com/pub/itk/Data/VisibleWomanHead/RawRGB/VisibleWomanHead.mhd



1.5) The reason why you don't find many examples on 3D
      segmentation in the Software Guide is because it
      was harder to find a way of presenting the results.

    However, almost all the segmentation methods in ITK
    are implemented for N-Dimensions. From the point of
    view of writing code, you can convert most of the
    examples in the software guide from 2D to 3D just by
    changing the template parameters of the Image type
    instantiation.

    You will find *many* examples in 3D segmentation in
    the InsightApplications checkout.

    In particular

      - RegionGrowing
      - FastMarchingLevelSet
      - ShapeDetectionLeveSet
      - GeodesicActiveContoursLeveSet
      - ThresholdSegmentationLevelSetFltkGui
      - Morphogenesis
      - SegmentationEditorFltkGui
      - DeformableModels
      - SNAP (Level Sets)
      - VolviewPlugins (many algorithms into VolView)
      - LiverTumorSegmentation

    Please look at the following page for description

      http://www.itk.org/HTML/Applications.htm

    The source code of InsightApplications can be downloaded
    in the same way that you downloaded "Insight".


2) You can use VTK for visualizing the scans from the
    Visible Human.  In practice, once you load the data
    set into an ITK image, then you can convert it into
    a vtkImageData and visualize it with VTK.

    You will find examples on this in

        InsightApplications/Auxiliary/vtk



3) Are you using Shared Libraries ?

    Did you built this example outside of the
    Insight tree ?

    What *exact* parameters did you passed in
    the command line when the example crashed ?

    Chances are that you are passing an inconsistent
    number (or values) of parameters to this example.

    Please post the exact command+arguments to the list.




Thanks


    Luis



------------------------
Jacob Boomgaarden wrote:

> Hi all,
> 
> I am working with a project to reconstruct a 3D model of the human lung
> from the Visible Human Project dataset and had a few questions regarding
> some segmentation usages. The application I will be making incorporates
> both ITK and VTK capabilities and, as of now, I am working with CT images
> while looking at using one or both of itkConfidenceConnectedImageFilter or
> itkFastMarchingImageFilter segmentation methods.
> 
> Here are some questions I have come up against:
> 
> 1)  When using either of the above segmentation methods, how do I go about
> first creating a 3-dimensional itk::Image out of the 2D CT scans to then
> segment? I realize that the algorithms allow for 3D segmentation and I
> would assume that this would be more efficient to use than by segmenting
> each individual 2D image first and then creating a 3D image out of those.
> The examples that I have run across in the ITK SoftwareGuide seem to only
> show how to do the segmentation on a 2D image. Are there any examples
> using segmentation on 3D images?
> 
> 2)  Allow I haven't looked too hard within VTK's capabilities, I am just
> curious as to whether (and then how) VTK is able to view the bitmap images
> of the CT scans from the Visible Humag Project dataset?
> 
> 3)  While running the example
> Examples/Segmentation/ConfidenceConnected.cxx I ran into a peculiar
> problem. The first time I ran the executable it worked just fine and
> segmented the suggested BrainProtonDensitySlice.png image. But when I
> tried running it again at a later point, it wouldn't finish properly and
> displayed the following error message:
> 
> Error: Segmentation Fault (core dumped)
> 
> Why would this not work the second (and numerous tries afterwards) time
> correctly?
> 
> Thanks for all your help and suggestions!
> 
>