[ITK] [ITK-users] Overlay Woes

[Becksfort, Jared]

 Hello,
   Sorry to send this again, but it had the wrong subject.

    I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):. https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html

    The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.

    Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.

    Thanks,
    Jared

    const unsigned int Dimension = 3;

    typedef float PixelType;
    typedef unsigned char LabelType;

    typedef itk::Image< PixelType, Dimension > ImageVolumeType;
    typedef itk::Image< LabelType, Dimension > ContourVolumeType;

    typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
    typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName( infile1 );

    ContourReaderType::Pointer labelReader = ContourReaderType::New();
    labelReader->SetFileName(infile2);

    typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
    typedef itk::LabelMap< LabelObjectType > LabelMapType;

    typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
    ConverterType::Pointer converter = ConverterType::New();
    converter->SetInput( labelReader->GetOutput() );

    typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
    FilterType::Pointer filter = FilterType::New();
    filter->SetInput( converter->GetOutput() );
    filter->SetFeatureImage( reader->GetOutput() );
    filter->SetOpacity(0.5);


    typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();
    writer->SetFileName(outfile);
    writer->SetInput( filter->GetOutput() );
    writer->Update();




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