typename TImage::Pointer modelBasedImageToImageRegistration(std::string referenceFilename, std::string targetFilename, typename TStatisticalModelType::Pointer model, std::string outputDfFilename, unsigned numberOfIterations){ typedef itk::ImageFileReader<TImage> ImageReaderType; typedef itk::InterpolatingStatisticalDeformationModelTransform<TRepresenter, double, VImageDimension> TransformType; typedef itk::LBFGSOptimizer OptimizerType; typedef itk::ImageRegistrationMethod<TImage, TImage> RegistrationFilterType; typedef itk::WarpImageFilter< TImage, TImage, TVectorImage > WarperType; typedef itk::LinearInterpolateImageFunction< TImage, double > InterpolatorType; typename ImageReaderType::Pointer referenceReader = ImageReaderType::New(); referenceReader->SetFileName(referenceFilename.c_str()); referenceReader->Update(); typename TImage::Pointer referenceImage = referenceReader->GetOutput(); referenceImage->Update(); typename ImageReaderType::Pointer targetReader = ImageReaderType::New(); targetReader->SetFileName(targetFilename.c_str()); targetReader->Update(); typename TImage::Pointer targetImage = targetReader->GetOutput(); targetImage->Update(); // do the fitting typename TransformType::Pointer transform = TransformType::New(); transform->SetStatisticalModel(model); transform->SetIdentity(); // Setting up the fitting OptimizerType::Pointer optimizer = OptimizerType::New(); optimizer->MinimizeOn(); optimizer->SetMaximumNumberOfFunctionEvaluations(numberOfIterations); typedef IterationStatusObserver ObserverType; ObserverType::Pointer observer = ObserverType::New(); optimizer->AddObserver( itk::IterationEvent(), observer ); typename TMetricType::Pointer metric = TMetricType::New(); typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); typename RegistrationFilterType::Pointer registration = RegistrationFilterType::New(); registration->SetInitialTransformParameters(transform->GetParameters()); registration->SetMetric(metric); registration->SetOptimizer( optimizer ); registration->SetTransform( transform ); registration->SetInterpolator( interpolator ); registration->SetFixedImage( targetImage ); registration->SetFixedImageRegion(targetImage->GetBufferedRegion() ); registration->SetMovingImage( referenceImage ); try { std::cout << "Performing registration... " << std::flush; registration->Update(); std::cout << "[done]" << std::endl; } catch ( itk::ExceptionObject& o ) { std::cout << "caught exception " << o << std::endl; } typename TVectorImage::Pointer df = model->DrawSample(transform->GetCoefficients()); // write deformation field if(outputDfFilename.size()>0){ typename itk::ImageFileWriter<TVectorImage>::Pointer df_writer = itk::ImageFileWriter<TVectorImage>::New(); df_writer->SetFileName(outputDfFilename); df_writer->SetInput(df); df_writer->Update(); } // warp reference std::cout << "Warping reference... " << std::flush; typename WarperType::Pointer warper = WarperType::New(); warper->SetInput(referenceImage ); warper->SetInterpolator( interpolator ); warper->SetOutputSpacing( targetImage->GetSpacing() ); warper->SetOutputOrigin( targetImage->GetOrigin() ); warper->SetOutputDirection( targetImage->GetDirection() ); warper->SetDisplacementField( df ); warper->Update(); std::cout << "[done]" << std::endl; return warper->GetOutput(); }