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List: insight-users
Subject: [ITK-users] Overlay Woes
From: "Becksfort, Jared" <Jared.Becksfort () STJUDE ! ORG>
Date: 2018-01-25 23:57:04
Message-ID: F3BC7CCC-FFCC-40E0-91F0-62ED15A5EB9A () stjude ! org
[Download RAW message or body]
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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