# Label Map Overlay Problem

**URL:** <https://discourse.itk.org/t/label-map-overlay-problem/628>\
**Category:** Beginner Questions\
**Created:** [January 26, 2018, 7:56pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628 "2018-01-26T19:56:17Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![jbcksfrt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/j/bbce88/32.png) [@jbcksfrt](https://discourse.itk.org/u/jbcksfrt)\
**Post date:** [January 26, 2018, 7:56pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/1 "2018-01-26T19:56:17Z")

</div>

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).

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 in ITK Snap

Thanks,
Jared

```

[https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html](https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html)

```
             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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<div class="post-metadata">

**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [January 28, 2018, 2:46pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/2 "2018-01-28T14:46:51Z")

</div>

Have you tried visualizing your output using [Slicer](https://www.slicer.org/)? I don’t remember whether ITK-SNAP supports RGB pixel types.

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**Author:** ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Post date:** [January 28, 2018, 10:13pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/3 "2018-01-28T22:13:04Z")

</div>

What is the range of your input image? I suspect the filter is doing a poor or unexpected job of mapping the ranges. I’d have to look at the filters source code to determine what is expects could me numeric traits min/max or 0-255. If you want the output to be 0-255 I’d scale the input of the overlay filter to that range.

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<div class="post-metadata">

**Author:** ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Post date:** [January 29, 2018, 4:14pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/4 "2018-01-29T16:14:21Z")

</div>

One more thing, I see you start with a “Label Image”. Have you looked at[LabelOverlayImageFilter](https://itk.org/Doxygen/html/classitk_1_1LabelOverlayImageFilter.html), it should do a similar operation with out having to convert to a “LabelMap” first.

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<div class="post-metadata">

**Author:** ![jbcksfrt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/j/bbce88/32.png) [@jbcksfrt](https://discourse.itk.org/u/jbcksfrt)\
**Post date:** [January 29, 2018, 4:24pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/5 "2018-01-29T16:24:41Z")

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Thank you both for the help so far. The type of my input image is float. I am rebuilding ITK to the latest version and will try your latest suggestions.

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<div class="post-metadata">

**Author:** ![jbcksfrt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/j/bbce88/32.png) [@jbcksfrt](https://discourse.itk.org/u/jbcksfrt)\
**Post date:** [January 29, 2018, 5:39pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/6 "2018-01-29T17:39:16Z")

</div>

![10 AM](https://discourse.itk.org/uploads/default/original/1X/9e0f9e197b9ea39766a3426014222655006a1052.png)

Slicer does not show it any better than ITK SNAP. I have attached an ITK SNAP screenshot showing that it is still a little messed up. This is probably very close, but I wonder if I have done something wrong with the RGB conversion.

Here is the code I used to generate it:

#include “itkBinaryImageToLabelMapFilter.h”  
#include “itkImage.h”  
#include “itkImageFileReader.h”  
#include “itkImageFileWriter.h”  
#include “itkImageRegionIterator.h”  
#include “itkLabelMapToLabelImageFilter.h”  
#include “itkLabelOverlayImageFilter.h”  
#include “itkRGBPixel.h”

using namespace std;

typedef itk::Image\<float, 3\> MriImageType;  
typedef itk::Image\<unsigned char, 3\> MaskImageType;

typedef itk::ImageFileReader MriReaderType;  
typedef itk::ImageFileReader MaskReaderType;

int main(int argc, char \*argv[])  
{

if (argc \< 4){  
cerr \<\< “mri, mask, output\_image” \<\< endl;  
return 1;  
}

string mri\_filename = argv[1];  
string mask\_filename = argv[2];  
string output\_filename = argv[3];

MriReaderType::Pointer mri\_reader = MriReaderType::New();  
mri\_reader-\>SetFileName(mri\_filename);  
MriImageType::Pointer mri\_image = mri\_reader-\>GetOutput(); // MriImageType::New();

MaskReaderType::Pointer mask\_reader = MaskReaderType::New();  
mask\_reader-\>SetFileName(mask\_filename);  
MaskImageType::Pointer mask\_image = mask\_reader-\>GetOutput(); // MaskImageType::New();

typedef itk::BinaryImageToLabelMapFilter BinaryImageToLabelMapFilterType;  
BinaryImageToLabelMapFilterType::Pointer binaryImageToLabelMapFilter = BinaryImageToLabelMapFilterType::New();  
binaryImageToLabelMapFilter-\>SetInput(mask\_image);  
binaryImageToLabelMapFilter-\>Update();

typedef itk::LabelMapToLabelImageFilter\<BinaryImageToLabelMapFilterType::OutputImageType, MaskImageType\> LabelMapToLabelImageFilterType;  
LabelMapToLabelImageFilterType::Pointer labelMapToLabelImageFilter = LabelMapToLabelImageFilterType::New();  
labelMapToLabelImageFilter-\>SetInput(binaryImageToLabelMapFilter-\>GetOutput());  
labelMapToLabelImageFilter-\>Update();  
typedef itk::RGBPixel RGBPixelType;  
typedef itk::Image\<RGBPixelType, 3\> RGBImageType;

typedef itk::LabelOverlayImageFilter\<MriImageType, MaskImageType, RGBImageType\>  
LabelOverlayImageFilterType;  
LabelOverlayImageFilterType::Pointer labelOverlayImageFilter = LabelOverlayImageFilterType::New();  
labelOverlayImageFilter-\>SetInput(mri\_image);  
labelOverlayImageFilter-\>SetLabelImage(labelMapToLabelImageFilter-\>GetOutput());  
labelOverlayImageFilter-\>SetOpacity(.5);  
labelOverlayImageFilter-\>Update();

typedef itk::ImageFileWriter\< RGBImageType \> WriterType;  
WriterType::Pointer writer = WriterType::New();  
writer-\>SetFileName(output\_filename);  
writer-\>SetInput(labelOverlayImageFilter-\>GetOutput());  
writer-\>Update();

return EXIT\_SUCCESS;  
}

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<div class="post-metadata">

**Author:** ![jbcksfrt](https://discourse.itk.org/letter_avatar_proxy/v4/letter/j/bbce88/32.png) [@jbcksfrt](https://discourse.itk.org/u/jbcksfrt)\
**Post date:** [February 12, 2018, 2:56pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/7 "2018-02-12T14:56:02Z")

</div>

Thank you for the help. It steered me in the right direction. I got it working with this code, which probably has some redundant lines (Updates and GetOutputs and so on) but helps make it clear to me at least:

```
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, 3> RGBImageType;

RGBImageType::Pointer overlayContour(ImageType::Pointer patient_image, BinaryImageType::Pointer segmented_image, const float opacity){

        // rescale patient volume
        typedef itk::RescaleIntensityImageFilter<ImageType, ImageType> RescaleFilterType;
        RescaleFilterType::Pointer rescale_filter= RescaleFilterType::New();
        rescale_filter->SetInput(patient_image);
        rescale_filter->SetOutputMinimum(0);
        rescale_filter->SetOutputMaximum(itk::NumericTraits<BinaryPixelType>::max());
        rescale_filter->Update();
        ImageType::Pointer rescaled = rescale_filter->GetOutput();

        // cast patient volume
        typedef itk::CastImageFilter<ImageType, BinaryImageType> CastFilterType;
        CastFilterType::Pointer cast_filter = CastFilterType::New();
        cast_filter->SetInput(rescaled);
        cast_filter->Update();
        BinaryImageType::Pointer casted = cast_filter->GetOutput();

        // convert label image to label map
        typedef itk::LabelObject<BinaryPixelType, 3> LabelObjectType;
        typedef itk::LabelMap<LabelObjectType> LabelMapType;

        typedef itk::LabelImageToLabelMapFilter<BinaryImageType, LabelMapType> ConverterType;
        ConverterType::Pointer converter = ConverterType::New();
        converter->SetInput(segmented_image);
        converter->Update();
        LabelMapType::Pointer converted = converter->GetOutput();

        // overlay contour on volume
        typedef itk::LabelMapOverlayImageFilter<LabelMapType, BinaryImageType> OverlayFilterType;
        OverlayFilterType::Pointer overlay_filter = OverlayFilterType::New();
        overlay_filter->SetInput(converted);
        overlay_filter->SetFeatureImage(casted);
        overlay_filter->SetOpacity(opacity);
        overlay_filter->Update();
        OverlayFilterType::OutputImageType::Pointer overlay_image = overlay_filter->GetOutput();

        return overlay_image;
}
```

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<div class="post-metadata">

**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [February 12, 2018, 3:43pm UTC](https://discourse.itk.org/t/label-map-overlay-problem/628/8 "2018-02-12T15:43:05Z")

</div>

Thanks for sharing your solution!