[Insight-users] Help with Connected Threshold Filter

[Wu Zheying]

Hi all,

I am doing connected threshold filter on a Analyze dataset. However, I keep on gettin black outputs no matter what threshold range and seed point i specify. Can someone help me out with this?

my input commands:

ConnectedThresholdImageFilter MRI2.hdr output.hdr 295 221 250 255 95

I initially placed my seed point at (221,250,95) where the image intensity is bright (250-255)

my code attached:

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
#include "itkCastImageFilter.h"
#include "itkCurvatureFlowImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


int main( int argc, char *argv[])
{
  if( argc < 8 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage  outputImage seedX seedY lowerThreshold upperThreshold  seedZ" << std::endl;
    return 1;
    }

  typedef   float         InternalPixelType;
  const     unsigned int    Dimension = 3;
  typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;

  typedef unsigned char OutputPixelType;
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
  typedef itk::CastImageFilter< InternalImageType, OutputImageType >
    CastFilterType;
  CastFilterType::Pointer caster = CastFilterType::New();
 
  typedef  itk::ImageFileReader< InternalImageType > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( argv[1] );
  
  writer->SetFileName( argv[2] );
 
  typedef itk::CurvatureFlowImageFilter< InternalImageType, InternalImageType >
    CurvatureFlowImageFilterType;

  CurvatureFlowImageFilterType::Pointer smoothing = 
                         CurvatureFlowImageFilterType::New();

  typedef itk::ConnectedThresholdImageFilter< InternalImageType, 
                                    InternalImageType > ConnectedFilterType;

  ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();

  smoothing->SetInput( reader->GetOutput() );
   
  connectedThreshold->SetInput( smoothing->GetOutput() );
  caster->SetInput (connectedThreshold->GetOutput());
  writer->SetInput ( caster->GetOutput());

  smoothing->SetNumberOfIterations( 1 );
  smoothing->SetTimeStep( 0.0625 );

  const InternalPixelType lowerThreshold = atof( argv[5] );
  const InternalPixelType upperThreshold = atof( argv[6] );

  connectedThreshold->SetLower(  lowerThreshold  );
  connectedThreshold->SetUpper(  upperThreshold  );

  connectedThreshold->SetReplaceValue( 255 );
 
  InternalImageType::IndexType  index;
  
  index[0] = atoi( argv[3] );
  index[1] = atoi( argv[4] );
  index[2] = atoi( argv[7] );

  connectedThreshold->SetSeed( index );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

  return 0;
}


Appreciate the help!

ZHeying


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