# Problem in binary image

**URL:** https://discourse.itk.org/t/problem-in-binary-image/2921
**Category:** Beginner Questions
**Created:** [April 10, 2020, 5:27pm UTC](https://discourse.itk.org/t/problem-in-binary-image/2921 "2020-04-10T17:27:48Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![basal](https://discourse.itk.org/letter_avatar_proxy/v4/letter/b/a8b319/32.png) [@basal](https://discourse.itk.org/u/basal)
#### Post date: [April 10, 2020, 5:27pm UTC](https://discourse.itk.org/t/problem-in-binary-image/2921/1 "2020-04-10T17:27:48Z")

</div>

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](https://discourse.itk.org/uploads/short-url/gl3t7M4Hg2PDmgYx9ePlK8H2aWl.nrrd) (377.8 KB)

```auto
#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;
}

```