Hi,
I used the following code for getting binary image, however, I am seeing some grayish spots on some slices. does anyone know what the problem is ? i also attached the resultant image.
outbinary.nrrd (377.8 KB)
#include "itkBinaryThresholdImageFilter.h"
// Software Guide : EndCodeSnippet
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
int main( int argc, char * argv[] )
{
if( argc < 7 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImageFile outputImageFile ";
std::cerr << " lowerThreshold upperThreshold ";
std::cerr << " outsideValue insideValue " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// The next step is to decide which pixel types to use for the input and output
// images.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InputPixelType = unsigned char;
using OutputPixelType = unsigned char;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input and output image types are now defined using their respective
// pixel types and dimensions.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InputImageType = itk::Image< InputPixelType, 3 >;
using OutputImageType = itk::Image< OutputPixelType, 3>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filter type can be instantiated using the input and output image
// types defined above.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FilterType = itk::BinaryThresholdImageFilter<
InputImageType, OutputImageType >;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An \doxygen{ImageFileReader} class is also instantiated in order to read
// image data from a file. (See Section \ref{sec:IO} on page
// \pageref{sec:IO} for more information about reading
// and writing data.)
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ReaderType = itk::ImageFileReader< InputImageType >;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An \doxygen{ImageFileWriter} is instantiated in order to write the output
// image to a file.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using WriterType = itk::ImageFileWriter< OutputImageType >;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Both the filter and the reader are created by invoking their \code{New()}
// methods and assigning the result to \doxygen{SmartPointer}s.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
WriterType::Pointer writer = WriterType::New();
writer->SetInput( filter->GetOutput() );
reader->SetFileName( argv[1] );
// Software Guide : BeginLatex
//
// The image obtained with the reader is passed as input to the
// BinaryThresholdImageFilter.
//
// \index{itk::Binary\-Threshold\-Image\-Filter!SetInput()}
// \index{itk::FileImageReader!GetOutput()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetInput( reader->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The method \code{SetOutsideValue()} defines the intensity value to be
// assigned to those pixels whose intensities are outside the range defined
// by the lower and upper thresholds. The method \code{SetInsideValue()}
// defines the intensity value to be assigned to pixels with intensities
// falling inside the threshold range.
//
// \index{itk::Binary\-Threshold\-Image\-Filter!SetOutsideValue()}
// \index{itk::Binary\-Threshold\-Image\-Filter!SetInsideValue()}
// \index{SetOutsideValue()!itk::Binary\-Threshold\-Image\-Filter}
// \index{SetInsideValue()!itk::Binary\-Threshold\-Image\-Filter}
//
// Software Guide : EndLatex
const OutputPixelType outsideValue = std::stoi( argv[5] );
const OutputPixelType insideValue = std::stoi( argv[6] );
// Software Guide : BeginCodeSnippet
filter->SetOutsideValue( outsideValue );
filter->SetInsideValue( insideValue );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The methods \code{SetLowerThreshold()} and \code{SetUpperThreshold()}
// define the range of the input image intensities that will be transformed
// into the \code{InsideValue}. Note that the lower and upper thresholds are
// values of the type of the input image pixels, while the inside and
// outside values are of the type of the output image pixels.
//
// Software Guide : EndLatex
const InputPixelType lowerThreshold = std::stoi( argv[3] );
const InputPixelType upperThreshold = std::stoi( argv[4] );
// Software Guide : BeginCodeSnippet
filter->SetLowerThreshold( lowerThreshold );
filter->SetUpperThreshold( upperThreshold );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The execution of the filter is triggered by invoking the \code{Update()}
// method. If the filter's output has been passed as input to subsequent
// filters, the \code{Update()} call on any downstream filters in the
// pipeline will indirectly trigger the update of this filter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.44\textwidth]{BinaryThresholdImageFilterOutput}
// \itkcaption[BinaryThresholdImageFilter output]{Effect of the BinaryThresholdImageFilter on a slice from a MRI
// proton density image of the brain.}
// \label{fig:BinaryThresholdImageFilterInputOutput}
// \end{figure}
//
// Figure \ref{fig:BinaryThresholdImageFilterInputOutput} illustrates the
// effect of this filter on a MRI proton density image of the brain. This
// figure shows the limitations of the filter for performing segmentation
// by itself. These limitations are particularly noticeable in noisy images
// and in images lacking spatial uniformity as is the case with MRI due to
// field bias.
//
// \relatedClasses
// \begin{itemize}
// \item \doxygen{ThresholdImageFilter}
// \end{itemize}
//
// Software Guide : EndLatex
writer->SetFileName( argv[2] );
writer->Update();
return EXIT_SUCCESS;
}