[Insight-users] Registration binary images

[Serena Fabbri]

Hi All,

I am registering binary images with 
Affine Transformation, MatchCardinality Metric, Amoeba optimizer, NearestNeighbor Interpolator.
When I set optimizerScales with  SetScales( optimizerScales ), I obtain this message independently by 
chosen values.

ExceptionObject caught !

itk::ExceptionObject (0x66d6a0)
Location: "typename itk::MatchCardinalityImageToImageMetric<TFixedImage, 
TMovingImage>::MeasureType itk::MatchCardinalityImageToImageMetric<TFixedImage, 
TMovingImage>::GetNonconstValue(const typename itk::ImageToImageMetric<TFixedImage, 
TMovingImage>::TransformParametersType&) [with TFixedImage = main(int, char**)::FixedImageType, 
TMovingImage = main(int, char**)::MovingImageType]" 
File: /Users/physics/InsightToolkit-
3.10.0/Code/Algorithms/itkMatchCardinalityImageToImageMetric.txx
Line: 130
Description: itk::ERROR: MatchCardinalityImageToImageMetric(0x6690c0): All the points mapped to 
outside of the moving image



If I don't set optimizerScales the registration starts but I have another problem.
I visualize the registration task with an observer with these 2 instruction:
std::cout << optimizer->GetCachedCurrentPosition()<< "   ";
std::cout << optimizer->GetCachedValue() ;

and it seems work but when I call
OptimizerType::ParametersType finalParameters =  registration->GetLastTransformParameters();
I get the initial parameters, so the output image is not registered.

does anyone experience with Affine Registration of binary image?
Could you give me any suggestion?
Thank you for any advice.
Serena.


this is the code:




// Metric

 	 metric->MeasureMatchesOff();

// Transform
   TransformInitializerType::Pointer initializer = TransformInitializerType::New();
   initializer->SetTransform(   transform );
   initializer->SetFixedImage(  fixedImageReader->GetOutput() );
   initializer->SetMovingImage( movingImageReader->GetOutput() );
   initializer->GeometryOn();
   initializer->InitializeTransform();


  //Optimizer
   unsigned int maxNumberOfIterations = 2000;

   if( argc > 3 )
     {
     maxNumberOfIterations = atoi( argv[4] );
     }

 	OptimizerType::ParametersType
     simplexDelta( transform->GetNumberOfParameters() );
 	simplexDelta.Fill( 10.0 );
 	std::cout<<"simplexDelta "<<simplexDelta<<std::endl;
 	std::cout<<"GetScales() "<<optimizer->GetScales()<<std::endl;
 	typedef OptimizerType::ScalesType       OptimizerScalesType;
 	OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );

 	optimizerScales[0] =  1.000;
 	optimizerScales[1] =  1.000;
 	optimizerScales[2] =  1.000;

 	optimizerScales[3] =  1.000;
 	optimizerScales[4] =  1.000;
 	optimizerScales[5] =  1.000;

 	optimizerScales[6] =  1.000;
 	optimizerScales[7] =  1.000;
 	optimizerScales[8] =  1.000;

 	double translationScale = 1.000;
 	optimizerScales[9] =  translationScale;
 	optimizerScales[10] =  translationScale;
 	optimizerScales[11] =  translationScale;

 	optimizer->SetScales( optimizerScales );
 	std::cout<<"GetScales() "<<optimizer->GetScales()<<std::endl;
 	optimizer->AutomaticInitialSimplexOff();
 	optimizer->SetInitialSimplexDelta( simplexDelta );
 	optimizer->SetParametersConvergenceTolerance( 0.25 ); // quarter pixel
 	optimizer->SetFunctionConvergenceTolerance(0.1); // 0.1%
     optimizer->SetMaximumNumberOfIterations(maxNumberOfIterations );

 	//Registration
 	registration->SetMetric(						metric        );
 	registration->SetOptimizer(						optimizer     );
 	registration->SetInterpolator(					interpolator  );
 	registration->SetTransform(						transform		);
 	registration->SetFixedImage(					fixedImageReader->GetOutput()    );
 	registration->SetMovingImage(					movingImageReader->GetOutput()   );
 	registration->SetFixedImageRegion(				fixedImageReader->GetOutput()-
>GetBufferedRegion() );
 	registration->SetInitialTransformParameters(	transform->GetParameters() );

 	// Osservatori
 	itkProbesCreate();
 	CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
 	optimizer->AddObserver( itk::IterationEvent(), observer);

  std::cout << std::endl << "Starting Affine Registration " << std::endl;
 	 std::cout <<	transform->GetNumberOfParameters()<< "  " << transform-
>GetParameters()<<std::endl;

 	try
     {
 		registration->Initialize();
 		std::cout << "Initial Metric value  = "<< metric->GetValue(transform-
>GetNumberOfParameters() ) << std::endl;
 		itkProbesStart( "Affine Registration " );
 		registration->StartRegistration();
 		itkProbesStop( "Affine Registration " );
     }
 	catch( itk::ExceptionObject & err )
     {
 		std::cerr << "ExceptionObject caught !" << std::endl;
 		std::cerr << err << std::endl;
 		return EXIT_FAILURE;
     }
 	// Report the time and memory taken by the registration
 	itkProbesReport( std::cout );


 	std::cout << "Affine Registration  completed" << std::endl;
 	std::cout << std::endl;




 	OptimizerType::ParametersType finalParameters =
                     registration->GetLastTransformParameters();

  	const double finalRotationCenterX = transform->GetCenter()[0];
 	const double finalRotationCenterY = transform->GetCenter()[1];
 	const double finalRotationCenterZ = transform->GetCenter()[2];
 	const double finalTranslationX    = finalParameters[9];
 	const double finalTranslationY    = finalParameters[10];
 	const double finalTranslationZ    = finalParameters[11];

 	const unsigned int numberOfIterations = optimizer->GetOptimizer()->get_num_evaluations();
 	const double bestValue = optimizer->GetValue();



   // Print out results

  	std::cout << "Result = " << std::endl;
 	std::cout << " Center X      = " << finalRotationCenterX  << std::endl;
 	std::cout << " Center Y      = " << finalRotationCenterY  << std::endl;
 	std::cout << " Center Z      = " << finalRotationCenterZ  << std::endl;
 	std::cout << " Translation X = " << finalTranslationX  << std::endl;
 	std::cout << " Translation Y = " << finalTranslationY  << std::endl;
 	std::cout << " Translation Z = " << finalTranslationZ  << std::endl;
 	std::cout << " Iterations    = " << numberOfIterations << std::endl;
 	std::cout << " Metric value  = " << bestValue          << std::endl;
 	std::cout << " finalParameters = "<<finalParameters<<std::endl;
   	std::cout << " finalParameters = "<<transform->GetParameters()<<std::endl;

//write time
   TransformType::Pointer finalTransform = TransformType::New();

   finalTransform->SetCenter( transform->GetCenter() );
   finalTransform->SetParameters( finalParameters );
   resampler->SetTransform( finalTransform );
   resampler->SetInput( movingImageReader->GetOutput() );

   FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();

   resampler->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
   resampler->SetOutputOrigin(  fixedImage->GetOrigin() );
   resampler->SetOutputSpacing( fixedImage->GetSpacing() );
   resampler->SetOutputDirection( fixedImage->GetDirection() );
   resampler->SetDefaultPixelValue( 0 );




   writer->SetFileName( argv[3] );
   caster->SetInput( resampler->GetOutput() );
   writer->SetInput( caster->GetOutput()   );


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