[Insight-users] visualization-problem after segmentation and cropping

[Luis Ibanez]

Hi Yusuf,


When you are debugging a pipeline you should
start by verifying that the data has been properly
loaded in memory, and then you should proceed
to check out the output of every intermediate filter
in order: from source to final output.


Please start by doing the following:


    Verify that you succeeded reading the DICOM series.

    Simply write the output of the Series reader to
    an output file.

    This essentially the code that you will see in
    the example:


    Insight/Examples/IO/
        DicomSeriesReadImageWrite2.cxx


    Open that file with any visualization software

    For example:

    1) Paraview. (http://www.paraview.org)  or
    2) Slicer, (http://www.slicer.org)  or
    3) SNAP, (http://sourceforge.net/projects/itk-snap/)  or
    4) VV (http://www.creatis.insa-lyon.fr/rio/vv)


Please let us know if you manage to do that initial
test, (it will be great if you post a screen shot of
that output image)

and then we will guide you to the next step.



    Regards,


         Luis


--------------------------------------------------
On Mon, May 24, 2010 at 10:26 PM, Yusuf OEZBEK <nasil122002 at yahoo.de> wrote:
> Hello,
>
>  I have a problem with cut (cropping) and visualization a 3D image, which I
> produced by the segmentation-method “watershed and region growing”. In the
> beginning I read the DICOM images with itkImageSeriesReader, then I run
> watershed or region growing algorithm, in order to connect itk with vtk and
> a 3D image produce and for the displaying of segmentation I use
> vtkContourFilter. After segmentation for cropping the images I use
> vtkBoxClipDataSet and vtkDataSetSurfaceFilter, but the result is a black
> screen.  When I read the images with vtkDICOMImageReader or
> itkImageSeriesReader and then segmented with volume rendering, marching
> cubes watershed and region growing, then it works completely well. The
> problem arises only when cut for watershed and region growing algorithm.
> What am I doing wrong?
>
> To understand my problem better, please see my screenshots on the following
> link.
>
>
>
> http://www.wopsys.com/bilder/segmentation.html
>
>
>
> To determine whether there missing of any geometrical informations. I had
> sent the following outputs of tests.
>
> http://www.wopsys.com/Outputs/Output_MarchingCubes.txt
> http://www.wopsys.com/Outputs/Output_VolumeRendering.txt
> http://www.wopsys.com/Outputs/Output_Watershed.txt
> http://www.wopsys.com/Outputs/Output_RegionGrowing.txt
>
> Thanks.
>
>
> ________________________________
> Von: Luis Ibanez <luis.ibanez at kitware.com>
> An: Yusuf OEZBEK <nasil122002 at yahoo.de>
> CC: ITK Mailinglist <insight-users at itk.org>; VTK Mailinglist
> <vtkusers at vtk.org>; nasil122002 at gmail.com
> Gesendet: Sonntag, den 18. April 2010, 1:12:33 Uhr
> Betreff: Re: [Insight-users] Cropping Problem
>
>
> Hi Yusuf,
>
>
> You should start by separating the segmentation
> problem from the visualization problem.
>
>
> Please do the following:
>
> 0) Just after you call:
>
>    reader->SetFileNames( fileNames );
>    reader->Update();
>
>    add
>
>    reader->GetOutput()->Print( std::cout );
>
>    then
>
> 1) Run the ITK segmentation pipeline until you
>     get the segmented image, and save it as a
>     MetaImage file (with extension .mhd)
>
>
> 2) Post the content of the resulting .mhd file
>     back to the list, as well as the print out of
>     the statement:
>
>    reader->GetOutput()->Print( std::cout );
>
>
> 3) Use Paraview (www.paraview.org) to load the
>     resulting image and extracting an iso-surface.
>     Compare that iso-surface with the one that
>     you get by directly from the DICOM image.
>     (and let us know what you find).
>
>
> With the information from (2) we should be
> able to identify if any geometrical information
> is missing from the ITK processing pipeline.
>
>
>    Thanks
>
>
>          Luis
>
>
>
>
>
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