[Insight-users] Managed ITK itkConfidenceConnectedImageFilter

[Luis Ibanez]

Hi Ali,

You may want to try the following segmentation filters:

        1) ConfidenceConnectedImageFilter

        2) IsolatedConnectedImageFilter

        3) ConnectedThresholdImageFilter

        4)  FastMarchingImageFilter


They are all variations of RegionGrowing filters,
for which you should provide some seed points
inside of the Jaw.


You will find these filters described in the
ITK Software Guide

       http://www.itk.org/ItkSoftwareGuide.pdf


In order to display the resulting segmentation,
you could use


A) VTK: See the examples in

InsightApplications/Auxiliary/vtk/
        itkReadITKImage3DExtractContourVTK.cxx
        itkReadITKImage3DSegmentShowVTK.cxx
        itkReadITKImageSegmentShowVTK.cxx
        itkReadITKImageShowSplineVTK.cxx
        itkReadITKImageShowVTK.cxx
        itkRegisterITKMonitorVTK.cxx


B) or you could use existing applications,
     such as


     1) Slicer (www.slicer.org)
     2) Paraview (www.paraview.org)



    Regards,


          Luis


------------------------------------------------------------------
On Tue, Feb 23, 2010 at 6:40 AM, Ali Habib <ali.mahmoud.habib at gmail.com> wrote:
> another question please
>
> If I work on DICOM series and want to segment in 3D
> the code will be
> itkImageBase
> input = itk.itkImage_UC3.New(); // This is your input image
> input.ReadDicomDirectory(
> @"");
> itkImageBase
> output = itk.itkImage_UC3.New(); // This is your output image
> itkConfidenceConnectedImageFilter
> filter =
> itkConfidenceConnectedImageFilter
> .New(input, output); // This willautomatically select the "IUC2IUC2" version
> of the filter
>
> is this true
>
> how can I reconstruct teh output of the segmentation in 3D (for example I
> want to extract the jaw and display it)
>
> any idea regards that
>
> On Tue, Feb 23, 2010 at 12:30 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>>
>> Hi Ali,
>>
>> It seems strange that you only get the following explicit types:
>> >> itkConfidenceConnectedImageFilter_IF2IF2
>> >> itkConfidenceConnectedImageFilter_IF3IF3
>> >> itkConfidenceConnectedImageFilter_ISS2ISS2
>> >> itkConfidenceConnectedImageFilter_IUC2IUC2
>>
>> When I build the latest ManagedITK (or look at the pre-built binaries
>> on the Google Code page) I see the following types:
>> itkConfidenceConnectedImageFilter_IF2IF2
>> itkConfidenceConnectedImageFilter_IF3IF3
>> itkConfidenceConnectedImageFilter_ISS2ISS2
>> itkConfidenceConnectedImageFilter_ISS3ISS3
>> itkConfidenceConnectedImageFilter_IUC2IUC2
>> itkConfidenceConnectedImageFilter_IUC3IUC3
>>
>> Regarding your question about how to create a new instance of the filter:
>>
>> There are two ways:
>>
>> 1. Decide the type at compile time. eg.
>> itkConfidenceConnectedImageFilter filter =
>> itkConfidenceConnectedImageFilter_IF2IF2.New();
>>
>> 2. Decide the type at run-time. eg.
>> itkImageBase input = itk.itkImage_UC2.New();
>> itkImageBase output = itk.itkImage_UC2.New();
>> // Select the IUC2IUC2 explicit type
>> itkConfidenceConnectedImageFilter filter =
>> itkConfidenceConnectedImageFilter.New(input, output);
>>
>> Hope this helps.
>>
>> Regards, Dan
>>
>> On 23 February 2010 10:24, Lodron, Gerald <Gerald.Lodron at joanneum.at>
>> wrote:
>> > Short is the same as signed short so you need:
>> >
>> > itkConfidenceConnectedImageFilter_ISS3ISS3
>> >
>> > if the class does not exist you must build it first for that image type
>> > (this classes are automatically build from the original templated C++
>> > classes)  but as i said i don't use managed code because of such
>> > problems
>> > and can't support you with that.
>> >
>> > A workaround would be to convert your image from short to float then you
>> > can
>> > use itkConfidenceConnectedImageFilter_IF3IF3, note that there already
>> > exists
>> > some caster classes in itk which will do that for you
>> > ________________________________
>> > Von: Ali Habib [mailto:ali.mahmoud.habib at gmail.com]
>> > Gesendet: Dienstag, 23. Februar 2010 10:17
>> > An: Lodron, Gerald
>> > Betreff: Re: [Insight-users] Managed ITK
>> > itkConfidenceConnectedImageFilter
>> >
>> >
>> > thanks for your reply
>> >
>> > What if my Input is DICOM series of type short , which type shall I do ,
>> > specially I want to segment in 3D
>> >
>> > Best regards
>> >
>> > On Tue, Feb 23, 2010 at 11:12 AM, Lodron, Gerald
>> > <Gerald.Lodron at joanneum.at>
>> > wrote:
>> >>
>> >> itkConfidenceConnectedImageFilter_IF2IF2  - input = 2D image of type
>> >> float, output = 2D image of type float
>> >> itkConfidenceConnectedImageFilter_IF3IF3  - input = 3D image of type
>> >> float, output =3D image of type float
>> >> itkConfidenceConnectedImageFilter_ISS2ISS2  - input = 2D image of type
>> >> signed short, output = 2D image of type signed short
>> >>
>> >> and so on....
>> >>
>> >> I don't use managed code because of this strange behaviour so i can't
>> >> give
>> >> you more support on error codes
>> >> ________________________________
>> >> Von: insight-users-bounces at itk.org
>> >> [mailto:insight-users-bounces at itk.org]
>> >> Im Auftrag von Ali Habib
>> >> Gesendet: Dienstag, 23. Februar 2010 09:39
>> >> An: insight-users at itk.org
>> >> Betreff: [Insight-users] Managed ITK itkConfidenceConnectedImageFilter
>> >>
>> >> I am trying to apply itkConfidenceConnectedImageFilter to image DICOM
>> >> series  , so I will use the watersheed example as guide
>> >>
>> >>
>> >> when use itkConfidenceConnectedImageFilter . it give error that this
>> >> class
>> >> can't be accessed due to its protection
>> >>
>> >> and discovered that there're 4 classes for
>> >> itkConfidenceConnectedImageFilter
>> >>
>> >> itkConfidenceConnectedImageFilter_IF2IF2
>> >> itkConfidenceConnectedImageFilter_IF3IF3
>> >> itkConfidenceConnectedImageFilter_ISS2ISS2
>> >> itkConfidenceConnectedImageFilter_IUC2IUC2
>> >>
>> >> I want to do
>> >> itkConfidenceConnectedImageFilter
>> >> x = new itkConfidenceConnectedImageFilter (input);   // input is the
>> >> itkimage that read the dicom series
>> >> and continue as in watersheed example
>> >> what's the difference between those classses
>> >> any suggestion please
>> >> Best regards
>
>
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