[Insight-users] Image-Registration Output-Direction

[Luis Ibanez]

Hi Yusuf,

Please see an example on how to do this in
the View2D class of the IGSTK toolkit,

http://public.kitware.com/cgi-bin/viewcvs.cgi/Source/igstkView2D.cxx?root=IGSTK&view=markup


Essentially you have to position your
vtkCamera according to:

http://www.itk.org/Wiki/Proposals:Orientation#DICOM_LPS_Orientation_-_Full_Body_Graphical_Example


      Regards,


            Luis


-----------------------------------------------------
On Sat, Dec 11, 2010 at 3:51 PM, Yusuf OEZBEK <nasil122002 at yahoo.de> wrote:
> Hallo,
>
> I wanted to have my MI-Registration in sagittal and coronal view. I made the
> registration in ITK and I presented it with VTK. But the output-direction is
> only in the axial-slice. How can I get the registration in sagittal and
> coronal view represent?
>
> Thanks
>
> Here is my Code:
>
>     const    unsigned int    Dimension = 2;
>     typedef  unsigned short  PixelType;
>
>     typedef itk::Image< PixelType, Dimension >  FixedImageType;
>     typedef itk::Image< PixelType, Dimension >  MovingImageType;
>
>     typedef itk::TranslationTransform< double, Dimension > TransformType;
>     typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
>     typedef itk::LinearInterpolateImageFunction< MovingImageType,double >
> InterpolatorType;
>     typedef itk::ImageRegistrationMethod<FixedImageType,MovingImageType>
> RegistrationType;
>
>     typedef
> itk::MattesMutualInformationImageToImageMetric<FixedImageType,MovingImageType
>> MetricType;
>
>     TransformType::Pointer transform= TransformType::New();
>     OptimizerType::Pointer  optimizer= OptimizerType::New();
>     InterpolatorType::Pointer interpolator= InterpolatorType::New();
>     RegistrationType::Pointer registration= RegistrationType::New();
>
>     registration->SetOptimizer(optimizer);
>     registration->SetTransform(transform);
>     registration->SetInterpolator(interpolator);
>
>     MetricType::Pointer metric = MetricType::New();
>     registration->SetMetric( metric  );
>
>     unsigned int numberOfBins = 24;
>     unsigned int numberOfSamples = 10000;
>
>     numberOfBins =24;
>     numberOfSamples =10000;
>
>     metric->SetNumberOfHistogramBins( numberOfBins );
>     metric->SetNumberOfSpatialSamples( numberOfSamples );
>     metric->SetUseExplicitPDFDerivatives(4);
>
>     typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
>     typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
>
>     FixedImageReaderType::Pointer  fixedImageReader  =
> FixedImageReaderType::New();
>     MovingImageReaderType::Pointer movingImageReader =
> MovingImageReaderType::New();
>
>
> //std::cout<<"pfad"<<filesSecondFusion.at((int)this->sliderFusion2->value()).c_str()<<endl;
>
>
> fixedImageReader->SetFileName(filesFirstFusion.at((int)this->sliderFusion1->value()).c_str());
>
> movingImageReader->SetFileName(filesSecondFusion.at((int)this->sliderFusion2->value()).c_str());
>
>     registration->SetFixedImage(fixedImageReader->GetOutput());
>     registration->SetMovingImage(movingImageReader->GetOutput());
>
>     fixedImageReader->Update();
>
>
> registration->SetFixedImageRegion(fixedImageReader->GetOutput()->GetBufferedRegion());
>
>     typedef RegistrationType::ParametersType ParametersType;
>     ParametersType initialParameters( transform->GetNumberOfParameters() );
>
>     initialParameters[0] = 0.0;  // Initial offset in mm along X
>     initialParameters[1] = 0.0;  // Initial offset in mm along Y
>
>     registration->SetInitialTransformParameters( initialParameters );
>
>     optimizer->MinimizeOn();
>     optimizer->SetMaximumStepLength(2.00);
>     optimizer->SetMinimumStepLength(0.001);
>     optimizer->SetNumberOfIterations(2000);
>     optimizer->SetRelaxationFactor(0.8);
>
>     ParametersType finalParameters =
> registration->GetLastTransformParameters();
>
>     double TranslationAlongX= finalParameters[0];
>     double TranslationAlongY= finalParameters[1];
>
>     unsigned int numberOfIterations = optimizer->GetCurrentIteration();
>
>     double bestValue = optimizer->GetValue();
>
>     std::cout << "Result = " << std::endl;
>     std::cout << " Translation X = " << TranslationAlongX  << std::endl;
>     std::cout << " Translation Y = " << TranslationAlongY  << std::endl;
>     std::cout << " Iterations    = " << numberOfIterations << std::endl;
>     std::cout << " Metric value  = " << bestValue          << std::endl;
>     std::cout << " Stop Condition  = " << optimizer->GetStopCondition() <<
> std::endl;
>
>
>     typedef itk::ResampleImageFilter<MovingImageType,FixedImageType>
> ResampleFilterType;
>
>     TransformType::Pointer finalTransform = TransformType::New();
>
>     finalTransform->SetParameters(finalParameters);
>     finalTransform->SetFixedParameters( transform->GetFixedParameters() );
>
>     ResampleFilterType::Pointer resample = ResampleFilterType::New();
>
>     resample->SetTransform( finalTransform );
>     resample->SetInput( movingImageReader->GetOutput() );
>
>     FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
>
>     PixelType defaultPixelValue= 100;
>     defaultPixelValue= 100;
>
>     resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
>     resample->SetOutputOrigin(fixedImage->GetOrigin());
>     resample->SetOutputSpacing(fixedImage->GetSpacing());
>     resample->SetOutputDirection(fixedImage->GetDirection());
>     resample->SetDefaultPixelValue(defaultPixelValue);
>
>
>     typedef  unsigned char  OutputPixelType;
>     typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
>     typedef itk::CastImageFilter<FixedImageType,OutputImageType>
> CastFilterType;
>     typedef itk::ImageFileWriter<OutputImageType>  WriterType;
>
>     WriterType::Pointer writer=  WriterType::New();
>     CastFilterType::Pointer caster=  CastFilterType::New();
>
>     writer->SetFileName("registration1.jpg");
>
>     caster->SetInput(resample->GetOutput());
>     writer->SetInput(caster->GetOutput());
>     writer->Update();
>
>     typedef itk::CheckerBoardImageFilter< FixedImageType >
> CheckerBoardFilterType;
>     CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New();
>
>     checker->SetInput1(fixedImage);
>     checker->SetInput2(resample->GetOutput());
>
>     if(imageRegistrationCheckerboardChoice->value()== 0){
>     unsigned int checkerArray[3]= {2,2,2};
>     checker->SetCheckerPattern(checkerArray);
>     }
>     if(imageRegistrationCheckerboardChoice->value()== 1){
>     unsigned int checkerArray[3]= {4,4,4};
>     checker->SetCheckerPattern(checkerArray);
>     }
>     if(imageRegistrationCheckerboardChoice->value()== 2){
>     unsigned int checkerArray[3]= {8,8,8};
>     checker->SetCheckerPattern(checkerArray);
>     }
>     if(imageRegistrationCheckerboardChoice->value()== 3){
>     unsigned int checkerArray[3]= {16,16,16};
>     checker->SetCheckerPattern(checkerArray);
>     }
>
>     caster->SetInput(checker->GetOutput());
>     writer->SetInput(caster->GetOutput() );
>
>     resample->SetDefaultPixelValue(100);
>
>     // Before registration
>     TransformType::Pointer identityTransform = TransformType::New();
>     identityTransform->SetIdentity();
>     resample->SetTransform( identityTransform );
>
>     writer->SetFileName("registration2.jpg");
>     writer->Update();
>
>
>       // After registration
>     resample->SetTransform( finalTransform );
>     writer->SetFileName("registration3.jpg");
>     writer->Update();
>
>     typedef itk::VTKImageExport< OutputImageType  > ExportFilterType;
>     ExportFilterType::Pointer itkExporter = ExportFilterType::New();
>     itkExporter->SetInput(caster->GetOutput() );
>
>     vtkImageImport* vtkImporter = vtkImageImport::New();
>     ConnectPipelines(itkExporter, vtkImporter);
>     vtkImporter->Update();
>
>     modeFusion = vtkInteractorStyleTrackballCamera::New();
>
>     rendererFusion = vtkRenderer::New();
>
>     renderWindowFusion = vtkRenderWindow::New();
>     renderWindowFusion->AddRenderer(rendererFusion);
>
>     imageFusionBox->SetRenderWindow(renderWindowFusion);
>     imageFusionBox->SetInteractorStyle(modeFusion);
>     imageFusionBox->Initialize();
>
>
>     imgFirstColorMap =  vtkLookupTable::New();
>     imgFirstColorMap->SetTableRange(-250, 1200);
>     imgFirstColorMap->SetSaturationRange(0,0);
>     imgFirstColorMap->SetHueRange(0, 0);
>     imgFirstColorMap->SetValueRange(0, 2);
>     imgFirstColorMap->Build();
>
>     firstColorMapper =  vtkImageMapToColors::New();
>     firstColorMapper->SetInput(vtkImporter->GetOutput());
>     firstColorMapper->SetLookupTable(imgFirstColorMap);
>
>     imgFusionMIActor = vtkImageActor::New();
>     imgFusionMIActor->SetInput(firstColorMapper->GetOutput());
>     imgFusionMIActor->SetOpacity(1.0);
>
>     cameraFusion = vtkCamera::New();
>     cameraFusion->SetViewUp(0, 0, -1);
>     cameraFusion->SetPosition(0, 1, 0);
>     cameraFusion->SetFocalPoint(0, 0, 0);
>     cameraFusion->ComputeViewPlaneNormal();
>     cameraFusion->Roll(-90);
>     cameraFusion->Azimuth(90);
>     cameraFusion->Roll(90);
>
>     rendererFusion->AddActor(imgFusionMIActor);
>     rendererFusion->SetActiveCamera(cameraFusion);
>     rendererFusion->ResetCamera();
>     cameraFusion->Dolly(1.7);
>     rendererFusion->ResetCameraClippingRange();
>
>
>
>
>
> Mit freundlichen Grüßen
> Yusuf ÖZBEK
>
>
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