diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp index 10c19232b0..061b06623f 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp @@ -1,953 +1,955 @@ #include "itkFitFibersToImageFilter.h" #include namespace itk{ FitFibersToImageFilter::FitFibersToImageFilter() : m_PeakImage(nullptr) , m_DiffImage(nullptr) , m_ScalarImage(nullptr) , m_MaskImage(nullptr) , m_FitIndividualFibers(true) , m_GradientTolerance(1e-5) , m_Lambda(0.1) , m_MaxIterations(20) , m_FiberSampling(10) , m_Coverage(0) , m_Overshoot(0) , m_RMSE(0.0) , m_FilterOutliers(false) , m_MeanWeight(1.0) , m_MedianWeight(1.0) , m_MinWeight(1.0) , m_MaxWeight(1.0) , m_Verbose(true) , m_DeepCopy(true) , m_ResampleFibers(true) , m_NumUnknowns(0) , m_NumResiduals(0) , m_NumCoveredDirections(0) , m_SignalModel(nullptr) , sz_x(0) , sz_y(0) , sz_z(0) , m_MeanTractDensity(0) , m_MeanSignal(0) , fiber_count(0) , m_Regularization(VnlCostFunction::REGU::VOXEL_VARIANCE) { this->SetNumberOfRequiredOutputs(3); } FitFibersToImageFilter::~FitFibersToImageFilter() { } void FitFibersToImageFilter::CreateDiffSystem() { sz_x = m_DiffImage->GetLargestPossibleRegion().GetSize(0); sz_y = m_DiffImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_DiffImage->GetLargestPossibleRegion().GetSize(2); dim_four_size = m_DiffImage->GetVectorLength(); int num_voxels = sz_x*sz_y*sz_z; float minSpacing = 1; if(m_DiffImage->GetSpacing()[0]GetSpacing()[1] && m_DiffImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_DiffImage->GetSpacing()[0]; else if (m_DiffImage->GetSpacing()[1] < m_DiffImage->GetSpacing()[2]) minSpacing = m_DiffImage->GetSpacing()[1]; else minSpacing = m_DiffImage->GetSpacing()[2]; if (m_ResampleFibers) for (unsigned int bundle=0; bundleGetDeepCopy(); m_Tractograms.at(bundle)->ResampleLinear(minSpacing/m_FiberSampling); std::cout.rdbuf (old); } m_NumResiduals = num_voxels * dim_four_size; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; m_NumCoveredDirections = 0; fiber_count = 0; vnl_vector voxel_indicator; voxel_indicator.set_size(sz_x*sz_y*sz_z); voxel_indicator.fill(0); m_GroupSizes.clear(); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!"; for (int j=0; jGetPoint(j); PointType3 p; p[0]=p1[0]; p[1]=p1[1]; p[2]=p1[2]; itk::Index<3> idx3; m_DiffImage->TransformPhysicalPointToIndex(p, idx3); if (!m_DiffImage->GetLargestPossibleRegion().IsInside(idx3) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0)) continue; double* p2 = points->GetPoint(j+1); mitk::DiffusionSignalModel<>::GradientType fiber_dir; fiber_dir[0] = p[0]-p2[0]; fiber_dir[1] = p[1]-p2[1]; fiber_dir[2] = p[2]-p2[2]; fiber_dir.Normalize(); int x = idx3[0]; int y = idx3[1]; int z = idx3[2]; mitk::DiffusionSignalModel<>::PixelType simulated_pixel = m_SignalModel->SimulateMeasurement(fiber_dir); VectorImgType::PixelType measured_pixel = m_DiffImage->GetPixel(idx3); double simulated_mean = 0; double measured_mean = 0; int num_nonzero_g = 0; for (int g=0; gGetGradientDirection(g).GetNorm()GetLargestPossibleRegion().GetSize(0); sz_y = m_PeakImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_PeakImage->GetLargestPossibleRegion().GetSize(2); dim_four_size = m_PeakImage->GetLargestPossibleRegion().GetSize(3)/3 + 1; // +1 for zero - peak int num_voxels = sz_x*sz_y*sz_z; float minSpacing = 1; if(m_PeakImage->GetSpacing()[0]GetSpacing()[1] && m_PeakImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_PeakImage->GetSpacing()[0]; else if (m_PeakImage->GetSpacing()[1] < m_PeakImage->GetSpacing()[2]) minSpacing = m_PeakImage->GetSpacing()[1]; else minSpacing = m_PeakImage->GetSpacing()[2]; if (m_ResampleFibers) for (unsigned int bundle=0; bundleGetDeepCopy(); m_Tractograms.at(bundle)->ResampleLinear(minSpacing/m_FiberSampling); std::cout.rdbuf (old); } m_NumResiduals = num_voxels * dim_four_size; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; m_NumCoveredDirections = 0; fiber_count = 0; m_GroupSizes.clear(); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!"; for (int j=0; jGetPoint(j); PointType4 p; p[0]=p1[0]; p[1]=p1[1]; p[2]=p1[2]; p[3]=0; itk::Index<4> idx4; m_PeakImage->TransformPhysicalPointToIndex(p, idx4); itk::Index<3> idx3; idx3[0] = idx4[0]; idx3[1] = idx4[1]; idx3[2] = idx4[2]; if (!m_PeakImage->GetLargestPossibleRegion().IsInside(idx4) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0)) continue; double* p2 = points->GetPoint(j+1); vnl_vector_fixed fiber_dir; fiber_dir[0] = p[0]-p2[0]; fiber_dir[1] = p[1]-p2[1]; fiber_dir[2] = p[2]-p2[2]; fiber_dir.normalize(); double w = 1; int peak_id = dim_four_size-1; - vnl_vector_fixed odf_peak = GetClosestPeak(idx4, m_PeakImage, fiber_dir, peak_id, w); - float peak_mag = odf_peak.magnitude(); + + double peak_mag = 0; + GetClosestPeak(idx4, m_PeakImage, fiber_dir, peak_id, w, peak_mag); int x = idx4[0]; int y = idx4[1]; int z = idx4[2]; unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z + sz_x*sz_y*sz_z*peak_id; if (b[linear_index] == 0 && peak_idGetLargestPossibleRegion().GetSize(0); sz_y = m_ScalarImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_ScalarImage->GetLargestPossibleRegion().GetSize(2); int num_voxels = sz_x*sz_y*sz_z; float minSpacing = 1; if(m_ScalarImage->GetSpacing()[0]GetSpacing()[1] && m_ScalarImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_ScalarImage->GetSpacing()[0]; else if (m_ScalarImage->GetSpacing()[1] < m_ScalarImage->GetSpacing()[2]) minSpacing = m_ScalarImage->GetSpacing()[1]; else minSpacing = m_ScalarImage->GetSpacing()[2]; if (m_ResampleFibers) for (unsigned int bundle=0; bundleGetDeepCopy(); m_Tractograms.at(bundle)->ResampleLinear(minSpacing/m_FiberSampling); std::cout.rdbuf (old); } m_NumResiduals = num_voxels; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; int numCoveredVoxels = 0; fiber_count = 0; m_GroupSizes.clear(); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j); PointType3 p; p[0]=p1[0]; p[1]=p1[1]; p[2]=p1[2]; itk::Index<3> idx3; m_ScalarImage->TransformPhysicalPointToIndex(p, idx3); if (!m_ScalarImage->GetLargestPossibleRegion().IsInside(idx3) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0)) continue; float image_value = m_ScalarImage->GetPixel(idx3); int x = idx3[0]; int y = idx3[1]; int z = idx3[2]; unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z; if (b[linear_index] == 0) { numCoveredVoxels++; m_MeanSignal += image_value; } m_MeanTractDensity += 1; if (m_FitIndividualFibers) { b[linear_index] = image_value; A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + 1); } else { b[linear_index] = image_value; A.put(linear_index, bundle, A.get(linear_index, bundle) + 1); } } ++fiber_count; } } m_MeanTractDensity /= (numCoveredVoxels*fiber_count); m_MeanSignal /= numCoveredVoxels; A /= m_MeanTractDensity; b *= 100.0/m_MeanSignal; // times 100 because we want to avoid too small values for computational reasons // NEW FIT -// m_MeanTractDensity /= numCoveredVoxels; -// m_MeanSignal /= numCoveredVoxels; -// b /= m_MeanSignal; -// b *= m_MeanTractDensity; + // m_MeanTractDensity /= numCoveredVoxels; + // m_MeanSignal /= numCoveredVoxels; + // b /= m_MeanSignal; + // b *= m_MeanTractDensity; } void FitFibersToImageFilter::GenerateData() { m_NumUnknowns = m_Tractograms.size(); if (m_FitIndividualFibers) { m_NumUnknowns = 0; for (unsigned int bundle=0; bundleGetNumFibers(); } else m_FilterOutliers = false; if (m_NumUnknowns<1) { MITK_INFO << "No fibers in tractogram."; return; } fiber_count = 0; sz_x = 0; sz_y = 0; sz_z = 0; m_MeanTractDensity = 0; m_MeanSignal = 0; if (m_PeakImage.IsNotNull()) CreatePeakSystem(); else if (m_DiffImage.IsNotNull()) CreateDiffSystem(); else if (m_ScalarImage.IsNotNull()) CreateScalarSystem(); else mitkThrow() << "No input image set!"; double init_lambda = fiber_count; // initialization for lambda estimation itk::TimeProbe clock; clock.Start(); cost = VnlCostFunction(m_NumUnknowns); cost.SetProblem(A, b, init_lambda, m_Regularization); cost.SetGroupSizes(m_GroupSizes); m_Weights.set_size(m_NumUnknowns); m_Weights.fill( 1.0/m_NumUnknowns ); vnl_lbfgsb minimizer(cost); vnl_vector l; l.set_size(m_NumUnknowns); l.fill(0); vnl_vector bound_selection; bound_selection.set_size(m_NumUnknowns); bound_selection.fill(1); minimizer.set_bound_selection(bound_selection); minimizer.set_lower_bound(l); minimizer.set_projected_gradient_tolerance(m_GradientTolerance); MITK_INFO << "Regularization type: " << m_Regularization; if (m_Regularization!=VnlCostFunction::REGU::NONE) // REMOVE FOR NEW FIT AND SET cost.m_Lambda = m_Lambda { MITK_INFO << "Estimating regularization"; minimizer.set_trace(false); minimizer.set_max_function_evals(2); minimizer.minimize(m_Weights); vnl_vector dx; dx.set_size(m_NumUnknowns); dx.fill(0.0); cost.calc_regularization_gradient(m_Weights, dx); - double r = dx.magnitude()/m_Weights.magnitude(); // wtf??? - cost.m_Lambda *= m_Lambda*55.0/r; - MITK_INFO << r << " - " << m_Lambda*55.0/r; - if (cost.m_Lambda>10e7) + + if (m_Weights.magnitude()==0) { MITK_INFO << "Regularization estimation failed. Using default value."; - cost.m_Lambda = fiber_count; + cost.m_Lambda = fiber_count*m_Lambda; + } + else + { + double r = dx.magnitude()/m_Weights.magnitude(); // wtf??? + cost.m_Lambda *= m_Lambda*55.0/r; + MITK_INFO << r << " - " << m_Lambda*55.0/r; + if (cost.m_Lambda>10e7) + { + MITK_INFO << "Regularization estimation failed. Using default value."; + cost.m_Lambda = fiber_count*m_Lambda; + } } } MITK_INFO << "Using regularization factor of " << cost.m_Lambda << " (λ: " << m_Lambda << ")"; MITK_INFO << "Fitting fibers"; minimizer.set_trace(m_Verbose); minimizer.set_max_function_evals(m_MaxIterations); minimizer.minimize(m_Weights); std::vector< double > weights; if (m_FilterOutliers) { for (auto w : m_Weights) weights.push_back(w); std::sort(weights.begin(), weights.end()); MITK_INFO << "Setting upper weight bound to " << weights.at(m_NumUnknowns*0.99); vnl_vector u; u.set_size(m_NumUnknowns); u.fill(weights.at(m_NumUnknowns*0.99)); minimizer.set_upper_bound(u); bound_selection.fill(2); minimizer.set_bound_selection(bound_selection); minimizer.minimize(m_Weights); weights.clear(); } for (auto w : m_Weights) weights.push_back(w); std::sort(weights.begin(), weights.end()); m_MeanWeight = m_Weights.mean(); m_MedianWeight = weights.at(m_NumUnknowns*0.5); m_MinWeight = weights.at(0); m_MaxWeight = weights.at(m_NumUnknowns-1); MITK_INFO << "*************************"; MITK_INFO << "Weight statistics"; MITK_INFO << "Sum: " << m_Weights.sum(); MITK_INFO << "Mean: " << m_MeanWeight; MITK_INFO << "1% quantile: " << weights.at(m_NumUnknowns*0.01); MITK_INFO << "5% quantile: " << weights.at(m_NumUnknowns*0.05); MITK_INFO << "25% quantile: " << weights.at(m_NumUnknowns*0.25); MITK_INFO << "Median: " << m_MedianWeight; MITK_INFO << "75% quantile: " << weights.at(m_NumUnknowns*0.75); MITK_INFO << "95% quantile: " << weights.at(m_NumUnknowns*0.95); MITK_INFO << "99% quantile: " << weights.at(m_NumUnknowns*0.99); MITK_INFO << "Min: " << m_MinWeight; MITK_INFO << "Max: " << m_MaxWeight; MITK_INFO << "*************************"; MITK_INFO << "NumEvals: " << minimizer.get_num_evaluations(); MITK_INFO << "NumIterations: " << minimizer.get_num_iterations(); MITK_INFO << "Residual cost: " << minimizer.get_end_error(); m_RMSE = cost.S->get_rms_error(m_Weights); MITK_INFO << "Final RMS: " << m_RMSE; clock.Stop(); int h = clock.GetTotal()/3600; int m = ((int)clock.GetTotal()%3600)/60; int s = (int)clock.GetTotal()%60; MITK_INFO << "Optimization took " << h << "h, " << m << "m and " << s << "s"; MITK_INFO << "Weighting fibers"; m_RmsDiffPerBundle.set_size(m_Tractograms.size()); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); if (m_FitIndividualFibers) { unsigned int fiber_count = 0; for (unsigned int bundle=0; bundle temp_weights; temp_weights.set_size(m_Weights.size()); temp_weights.copy_in(m_Weights.data_block()); for (int i=0; iGetNumFibers(); i++) { m_Tractograms.at(bundle)->SetFiberWeight(i, m_Weights[fiber_count]); temp_weights[fiber_count] = 0; ++fiber_count; } double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE; m_RmsDiffPerBundle[bundle] = d_rms; m_Tractograms.at(bundle)->Compress(0.1); m_Tractograms.at(bundle)->ColorFibersByFiberWeights(false, true); } } else { for (unsigned int i=0; i temp_weights; temp_weights.set_size(m_Weights.size()); temp_weights.copy_in(m_Weights.data_block()); temp_weights[i] = 0; double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE; m_RmsDiffPerBundle[i] = d_rms; m_Tractograms.at(i)->SetFiberWeights(m_Weights[i]); m_Tractograms.at(i)->Compress(0.1); m_Tractograms.at(i)->ColorFibersByFiberWeights(false, true); } } std::cout.rdbuf (old); // transform back A *= m_MeanSignal/100.0; b *= m_MeanSignal/100.0; MITK_INFO << "Generating output images ..."; if (m_PeakImage.IsNotNull()) GenerateOutputPeakImages(); else if (m_DiffImage.IsNotNull()) GenerateOutputDiffImages(); else if (m_ScalarImage.IsNotNull()) GenerateOutputScalarImages(); m_Coverage = m_Coverage/m_MeanSignal; m_Overshoot = m_Overshoot/m_MeanSignal; MITK_INFO << std::fixed << "Coverage: " << setprecision(2) << 100.0*m_Coverage << "%"; MITK_INFO << std::fixed << "Overshoot: " << setprecision(2) << 100.0*m_Overshoot << "%"; } void FitFibersToImageFilter::GenerateOutputDiffImages() { VectorImgType::PixelType pix; pix.SetSize(m_DiffImage->GetVectorLength()); pix.Fill(0); itk::ImageDuplicator< VectorImgType >::Pointer duplicator = itk::ImageDuplicator< VectorImgType >::New(); duplicator->SetInputImage(m_DiffImage); duplicator->Update(); m_UnderexplainedImageDiff = duplicator->GetOutput(); m_UnderexplainedImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_UnderexplainedImageDiff); duplicator->Update(); m_OverexplainedImageDiff = duplicator->GetOutput(); m_OverexplainedImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_OverexplainedImageDiff); duplicator->Update(); m_ResidualImageDiff = duplicator->GetOutput(); m_ResidualImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_ResidualImageDiff); duplicator->Update(); m_FittedImageDiff = duplicator->GetOutput(); m_FittedImageDiff->FillBuffer(pix); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); itk::ImageRegionIterator it1 = itk::ImageRegionIterator(m_DiffImage, m_DiffImage->GetLargestPossibleRegion()); itk::ImageRegionIterator it2 = itk::ImageRegionIterator(m_FittedImageDiff, m_FittedImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it3 = itk::ImageRegionIterator(m_ResidualImageDiff, m_ResidualImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it4 = itk::ImageRegionIterator(m_UnderexplainedImageDiff, m_UnderexplainedImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it5 = itk::ImageRegionIterator(m_OverexplainedImageDiff, m_OverexplainedImageDiff->GetLargestPossibleRegion()); m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; while( !it2.IsAtEnd() ) { itk::Index<3> idx3 = it2.GetIndex(); VectorImgType::PixelType original_pix =it1.Get(); VectorImgType::PixelType fitted_pix =it2.Get(); VectorImgType::PixelType residual_pix =it3.Get(); VectorImgType::PixelType underexplained_pix =it4.Get(); VectorImgType::PixelType overexplained_pix =it5.Get(); int num_nonzero_g = 0; double original_mean = 0; for (int g=0; gGetGradientDirection(g).GetNorm()>=mitk::eps ) { original_mean += original_pix[g]; ++num_nonzero_g; } } original_mean /= num_nonzero_g; for (int g=0; g=0) { underexplained_pix[g] = residual_pix[g]; m_Coverage += fitted_b[linear_index] + original_mean; } m_MeanSignal += b[linear_index] + original_mean; } it2.Set(fitted_pix); it3.Set(residual_pix); it4.Set(underexplained_pix); it5.Set(overexplained_pix); ++it1; ++it2; ++it3; ++it4; ++it5; } } void FitFibersToImageFilter::GenerateOutputScalarImages() { itk::ImageDuplicator< DoubleImgType >::Pointer duplicator = itk::ImageDuplicator< DoubleImgType >::New(); duplicator->SetInputImage(m_ScalarImage); duplicator->Update(); m_UnderexplainedImageScalar = duplicator->GetOutput(); m_UnderexplainedImageScalar->FillBuffer(0); duplicator->SetInputImage(m_UnderexplainedImageScalar); duplicator->Update(); m_OverexplainedImageScalar = duplicator->GetOutput(); m_OverexplainedImageScalar->FillBuffer(0); duplicator->SetInputImage(m_OverexplainedImageScalar); duplicator->Update(); m_ResidualImageScalar = duplicator->GetOutput(); m_ResidualImageScalar->FillBuffer(0); duplicator->SetInputImage(m_ResidualImageScalar); duplicator->Update(); m_FittedImageScalar = duplicator->GetOutput(); m_FittedImageScalar->FillBuffer(0); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); itk::ImageRegionIterator it1 = itk::ImageRegionIterator(m_ScalarImage, m_ScalarImage->GetLargestPossibleRegion()); itk::ImageRegionIterator it2 = itk::ImageRegionIterator(m_FittedImageScalar, m_FittedImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it3 = itk::ImageRegionIterator(m_ResidualImageScalar, m_ResidualImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it4 = itk::ImageRegionIterator(m_UnderexplainedImageScalar, m_UnderexplainedImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it5 = itk::ImageRegionIterator(m_OverexplainedImageScalar, m_OverexplainedImageScalar->GetLargestPossibleRegion()); m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; while( !it2.IsAtEnd() ) { itk::Index<3> idx3 = it2.GetIndex(); DoubleImgType::PixelType original_pix =it1.Get(); DoubleImgType::PixelType fitted_pix =it2.Get(); DoubleImgType::PixelType residual_pix =it3.Get(); DoubleImgType::PixelType underexplained_pix =it4.Get(); DoubleImgType::PixelType overexplained_pix =it5.Get(); unsigned int linear_index = idx3[0] + sz_x*idx3[1] + sz_x*sz_y*idx3[2]; fitted_pix = fitted_b[linear_index]; residual_pix = original_pix - fitted_pix; if (residual_pix<0) { overexplained_pix = residual_pix; m_Coverage += b[linear_index]; m_Overshoot -= residual_pix; } else if (residual_pix>=0) { underexplained_pix = residual_pix; m_Coverage += fitted_b[linear_index]; } m_MeanSignal += b[linear_index]; it2.Set(fitted_pix); it3.Set(residual_pix); it4.Set(underexplained_pix); it5.Set(overexplained_pix); ++it1; ++it2; ++it3; ++it4; ++it5; } } VnlCostFunction::REGU FitFibersToImageFilter::GetRegularization() const { return m_Regularization; } void FitFibersToImageFilter::SetRegularization(const VnlCostFunction::REGU &Regularization) { m_Regularization = Regularization; } void FitFibersToImageFilter::GenerateOutputPeakImages() { itk::ImageDuplicator< PeakImgType >::Pointer duplicator = itk::ImageDuplicator< PeakImgType >::New(); duplicator->SetInputImage(m_PeakImage); duplicator->Update(); m_UnderexplainedImage = duplicator->GetOutput(); m_UnderexplainedImage->FillBuffer(0.0); duplicator->SetInputImage(m_UnderexplainedImage); duplicator->Update(); m_OverexplainedImage = duplicator->GetOutput(); m_OverexplainedImage->FillBuffer(0.0); duplicator->SetInputImage(m_OverexplainedImage); duplicator->Update(); m_ResidualImage = duplicator->GetOutput(); m_ResidualImage->FillBuffer(0.0); duplicator->SetInputImage(m_ResidualImage); duplicator->Update(); m_FittedImage = duplicator->GetOutput(); m_FittedImage->FillBuffer(0.0); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); for (unsigned int r=0; r idx4; unsigned int linear_index = r; idx4[0] = linear_index % sz_x; linear_index /= sz_x; idx4[1] = linear_index % sz_y; linear_index /= sz_y; idx4[2] = linear_index % sz_z; linear_index /= sz_z; int peak_id = linear_index % dim_four_size; if (peak_id peak_dir; idx4[3] = peak_id*3; peak_dir[0] = m_PeakImage->GetPixel(idx4); idx4[3] += 1; peak_dir[1] = m_PeakImage->GetPixel(idx4); idx4[3] += 1; peak_dir[2] = m_PeakImage->GetPixel(idx4); peak_dir.normalize(); peak_dir *= fitted_b[r]; idx4[3] = peak_id*3; m_FittedImage->SetPixel(idx4, peak_dir[0]); idx4[3] += 1; m_FittedImage->SetPixel(idx4, peak_dir[1]); idx4[3] += 1; m_FittedImage->SetPixel(idx4, peak_dir[2]); } } m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; itk::Index<4> idx4; for (idx4[0]=0; idx4[0] idx3; idx3[0] = idx4[0]; idx3[1] = idx4[1]; idx3[2] = idx4[2]; if (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0) continue; vnl_vector_fixed peak_dir; vnl_vector_fixed fitted_dir; vnl_vector_fixed overshoot_dir; for (idx4[3]=0; idx4[3]<(itk::IndexValueType)m_PeakImage->GetLargestPossibleRegion().GetSize(3); ++idx4[3]) { peak_dir[idx4[3]%3] = m_PeakImage->GetPixel(idx4); fitted_dir[idx4[3]%3] = m_FittedImage->GetPixel(idx4); m_ResidualImage->SetPixel(idx4, m_PeakImage->GetPixel(idx4) - m_FittedImage->GetPixel(idx4)); if (idx4[3]%3==2) { m_MeanSignal += peak_dir.magnitude(); itk::Index<4> tidx= idx4; if (peak_dir.magnitude()>fitted_dir.magnitude()) { m_Coverage += fitted_dir.magnitude(); m_UnderexplainedImage->SetPixel(tidx, peak_dir[2]-fitted_dir[2]); tidx[3]--; m_UnderexplainedImage->SetPixel(tidx, peak_dir[1]-fitted_dir[1]); tidx[3]--; m_UnderexplainedImage->SetPixel(tidx, peak_dir[0]-fitted_dir[0]); } else { overshoot_dir[0] = fitted_dir[0]-peak_dir[0]; overshoot_dir[1] = fitted_dir[1]-peak_dir[1]; overshoot_dir[2] = fitted_dir[2]-peak_dir[2]; m_Coverage += peak_dir.magnitude(); m_Overshoot += overshoot_dir.magnitude(); m_OverexplainedImage->SetPixel(tidx, overshoot_dir[2]); tidx[3]--; m_OverexplainedImage->SetPixel(tidx, overshoot_dir[1]); tidx[3]--; m_OverexplainedImage->SetPixel(tidx, overshoot_dir[0]); } } } } } -vnl_vector_fixed FitFibersToImageFilter::GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed fiber_dir, int& id, double& w ) +void FitFibersToImageFilter::GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed fiber_dir, int& id, double& w, double& peak_mag ) { int m_NumDirs = peak_image->GetLargestPossibleRegion().GetSize()[3]/3; vnl_vector_fixed out_dir; out_dir.fill(0); float angle = 0.9; for (int i=0; i dir; idx[3] = i*3; dir[0] = peak_image->GetPixel(idx); idx[3] += 1; dir[1] = peak_image->GetPixel(idx); idx[3] += 1; dir[2] = peak_image->GetPixel(idx); float mag = dir.magnitude(); if (magangle) + float a = fabs(dot_product(dir, fiber_dir))/mag; + if (a>angle) { - angle = fabs(a); + angle = a; w = angle; - if (a<0) - out_dir = -dir; - else - out_dir = dir; - out_dir *= mag; + peak_mag = mag; id = i; } } - - return out_dir; } std::vector FitFibersToImageFilter::GetTractograms() const { return m_Tractograms; } void FitFibersToImageFilter::SetTractograms(const std::vector &tractograms) { m_Tractograms = tractograms; } void FitFibersToImageFilter::SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel) { m_SignalModel = SignalModel; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h index 81da7ebb77..e5d56fe256 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h @@ -1,483 +1,483 @@ #ifndef __itkFitFibersToImageFilter_h__ #define __itkFitFibersToImageFilter_h__ // MITK #include #include #include #include #include #include #include #include #include #include #include class VnlCostFunction : public vnl_cost_function { public: enum REGU { MSM, VARIANCE, LASSO, VOXEL_VARIANCE, GROUP_LASSO, GROUP_VARIANCE, NONE }; vnl_sparse_matrix_linear_system< double >* S; vnl_sparse_matrix< double > m_A; vnl_sparse_matrix< double > m_A_Ones; // matrix indicating active weights with 1 vnl_vector< double > m_b; double m_Lambda; // regularization factor vnl_vector row_sums; // number of active weights per row vnl_vector local_weight_means; // mean weight of each row REGU regularization; std::vector group_sizes; void SetProblem(vnl_sparse_matrix< double >& A, vnl_vector& b, double lambda, REGU regu) { S = new vnl_sparse_matrix_linear_system(A, b); m_A = A; m_b = b; m_Lambda = lambda; m_A_Ones.set_size(m_A.rows(), m_A.cols()); m_A.reset(); while (m_A.next()) m_A_Ones.put(m_A.getrow(), m_A.getcolumn(), 1); unsigned int N = m_b.size(); vnl_vector ones; ones.set_size(dim); ones.fill(1.0); row_sums.set_size(N); m_A_Ones.mult(ones, row_sums); local_weight_means.set_size(N); regularization = regu; } void SetGroupSizes(std::vector sizes) { unsigned int sum = 0; for (auto s : sizes) sum += s; if (sum!=m_A.cols()) { MITK_INFO << "Group sizes do not match number of unknowns (" << sum << " vs. " << m_A.cols() << ")"; return; } group_sizes = sizes; } VnlCostFunction(const int NumVars=0) : vnl_cost_function(NumVars) { } // Regularization: mean squared magnitude of weight vectors (small weights) void regu_MSM(vnl_vector const &x, double& cost) { cost += 10000.0*m_Lambda*x.squared_magnitude()/dim; } // Regularization: mean squared deaviation of weights from mean weight (enforce uniform weights) void regu_Variance(vnl_vector const &x, double& cost) { double mean = x.mean(); vnl_vector tx = x-mean; cost += 10000.0*m_Lambda*tx.squared_magnitude()/dim; } // Regularization: mean absolute magnitude of weight vectors (small weights) L1 void regu_Lasso(vnl_vector const &x, double& cost) { - cost += 10000.0*m_Lambda*x.one_norm()/dim; + cost += m_Lambda*x.one_norm()/dim; } // Regularization: mean squared deaviation of weights from bundle mean weight (enforce uniform weights PER BUNDLE) void regu_GroupVariance(vnl_vector const &x, double& cost) { vnl_vector tx(x); unsigned int offset = 0; for (auto g : group_sizes) { double group_mean = 0; for (unsigned int i=0; i const &x, double& cost) { m_A_Ones.mult(x, local_weight_means); local_weight_means = element_quotient(local_weight_means, row_sums); m_A_Ones.reset(); double regu = 0; while (m_A_Ones.next()) { double d = 0; if (x[m_A_Ones.getcolumn()]>local_weight_means[m_A_Ones.getrow()]) d = std::exp(x[m_A_Ones.getcolumn()]) - std::exp(local_weight_means[m_A_Ones.getrow()]); else d = x[m_A_Ones.getcolumn()] - local_weight_means[m_A_Ones.getrow()]; regu += d*d; } cost += m_Lambda*regu/dim; } // Regularization: group Lasso: sum_g(lambda_g * ||x_g||_2) void regu_GroupLasso(vnl_vector const &x, double& cost) { unsigned int offset = 0; for (auto g : group_sizes) { double group_cost = 0; for (unsigned int i=0; i const &x, vnl_vector &dx) { dx += 10000.0*m_Lambda*2.0*x/dim; } void grad_regu_Variance(vnl_vector const &x, vnl_vector &dx) { double mean = x.mean(); vnl_vector tx = x-mean; // difference to mean dx += 10000.0*tx*(2.0-2.0/dim)/dim; } void grad_regu_Lasso(vnl_vector const &x, vnl_vector &dx) { for (int i=0; i0) - dx[i] += 10000.0*m_Lambda/dim; + dx[i] += m_Lambda/dim; } void grad_regu_GroupVariance(vnl_vector const &x, vnl_vector &dx) { vnl_vector tx(x); unsigned int offset = 0; for (auto g : group_sizes) { double group_mean = 0; for (unsigned int i=0; i const &x, vnl_vector &dx) { m_A_Ones.mult(x, local_weight_means); local_weight_means = element_quotient(local_weight_means, row_sums); vnl_vector exp_x = x.apply(std::exp); vnl_vector exp_means = local_weight_means.apply(std::exp); vnl_vector tdx(dim, 0); m_A_Ones.reset(); while (m_A_Ones.next()) { int c = m_A_Ones.getcolumn(); int r = m_A_Ones.getrow(); if (x[c]>local_weight_means[r]) tdx[c] += exp_x[c] * ( exp_x[c] - exp_means[r] ); else tdx[c] += x[c] - local_weight_means[r]; } dx += tdx*2.0*m_Lambda/dim; } void grad_regu_GroupLasso(vnl_vector const &x, vnl_vector &dx) { unsigned int offset = 0; for (auto g : group_sizes) { double group_lambda = m_Lambda*std::sqrt(g)/dim; double group_l2 = 0; for (unsigned int i=0; i0.0) { for (unsigned int i=0; i const &x, double& cost) { if (regularization==VOXEL_VARIANCE) regu_VoxelVariance(x, cost); else if (regularization==VARIANCE) regu_Variance(x, cost); else if (regularization==MSM) regu_MSM(x, cost); else if (regularization==LASSO) regu_Lasso(x, cost); else if (regularization==GROUP_LASSO) regu_GroupLasso(x, cost); else if (regularization==GROUP_VARIANCE) regu_GroupVariance(x, cost); } void calc_regularization_gradient(vnl_vector const &x, vnl_vector &dx) { if (regularization==VOXEL_VARIANCE) grad_regu_VoxelVariance(x,dx); else if (regularization==VARIANCE) grad_regu_Variance(x,dx); else if (regularization==MSM) grad_regu_MSM(x,dx); else if (regularization==LASSO) grad_regu_Lasso(x,dx); else if (regularization==GROUP_LASSO) grad_regu_GroupLasso(x, dx); else if (regularization==GROUP_VARIANCE) grad_regu_GroupVariance(x, dx); } // cost function double f(vnl_vector const &x) { // RMS error unsigned int N = m_b.size(); vnl_vector d; d.set_size(N); S->multiply(x,d); double cost = (d - m_b).squared_magnitude()/N; // regularize calc_regularization(x, cost); return cost; } // gradient of cost function void gradf(vnl_vector const &x, vnl_vector &dx) { dx.fill(0.0); unsigned int N = m_b.size(); // calculate output difference d vnl_vector d; d.set_size(N); S->multiply(x,d); d -= m_b; // (f(u(x)))' = f'(u(x)) * u'(x) // d/dx_j = 1/N * Sum_i A_i,j * 2*(A_i,j * x_j - b_i) S->transpose_multiply(d, dx); dx *= 2.0/N; calc_regularization_gradient(x,dx); } }; namespace itk{ /** * \brief Fits the tractogram to the input image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092). */ class FitFibersToImageFilter : public ImageSource< mitk::PeakImage::ItkPeakImageType > { public: typedef FitFibersToImageFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Point PointType3; typedef itk::Point PointType4; typedef mitk::DiffusionPropertyHelper::ImageType VectorImgType; typedef mitk::PeakImage::ItkPeakImageType PeakImgType; typedef itk::Image UcharImgType; typedef itk::Image DoubleImgType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( FitFibersToImageFilter, ImageSource ) itkSetMacro( ScalarImage, DoubleImgType::Pointer) itkGetMacro( ScalarImage, DoubleImgType::Pointer) itkSetMacro( PeakImage, PeakImgType::Pointer) itkGetMacro( PeakImage, PeakImgType::Pointer) itkSetMacro( DiffImage, VectorImgType::Pointer) itkGetMacro( DiffImage, VectorImgType::Pointer) itkSetMacro( MaskImage, UcharImgType::Pointer) itkGetMacro( MaskImage, UcharImgType::Pointer) itkSetMacro( FitIndividualFibers, bool) itkGetMacro( FitIndividualFibers, bool) itkSetMacro( GradientTolerance, double) itkGetMacro( GradientTolerance, double) itkSetMacro( Lambda, double) itkGetMacro( Lambda, double) itkSetMacro( MaxIterations, int) itkGetMacro( MaxIterations, int) itkSetMacro( FiberSampling, float) itkGetMacro( FiberSampling, float) itkSetMacro( FilterOutliers, bool) itkGetMacro( FilterOutliers, bool) itkSetMacro( Verbose, bool) itkGetMacro( Verbose, bool) itkSetMacro( DeepCopy, bool) itkGetMacro( DeepCopy, bool) itkSetMacro( ResampleFibers, bool) itkGetMacro( ResampleFibers, bool) itkGetMacro( Weights, vnl_vector) itkGetMacro( RmsDiffPerBundle, vnl_vector) itkGetMacro( FittedImage, PeakImgType::Pointer) itkGetMacro( ResidualImage, PeakImgType::Pointer) itkGetMacro( OverexplainedImage, PeakImgType::Pointer) itkGetMacro( UnderexplainedImage, PeakImgType::Pointer) itkGetMacro( FittedImageDiff, VectorImgType::Pointer) itkGetMacro( ResidualImageDiff, VectorImgType::Pointer) itkGetMacro( OverexplainedImageDiff, VectorImgType::Pointer) itkGetMacro( UnderexplainedImageDiff, VectorImgType::Pointer) itkGetMacro( FittedImageScalar, DoubleImgType::Pointer) itkGetMacro( ResidualImageScalar, DoubleImgType::Pointer) itkGetMacro( OverexplainedImageScalar, DoubleImgType::Pointer) itkGetMacro( UnderexplainedImageScalar, DoubleImgType::Pointer) itkGetMacro( Coverage, double) itkGetMacro( Overshoot, double) itkGetMacro( RMSE, double) itkGetMacro( MeanWeight, double) itkGetMacro( MedianWeight, double) itkGetMacro( MinWeight, double) itkGetMacro( MaxWeight, double) itkGetMacro( NumUnknowns, unsigned int) itkGetMacro( NumResiduals, unsigned int) itkGetMacro( NumCoveredDirections, unsigned int) void SetTractograms(const std::vector &tractograms); void GenerateData() override; std::vector GetTractograms() const; void SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel); VnlCostFunction::REGU GetRegularization() const; void SetRegularization(const VnlCostFunction::REGU &GetRegularization); protected: FitFibersToImageFilter(); virtual ~FitFibersToImageFilter(); - vnl_vector_fixed GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer m_PeakImage , vnl_vector_fixed fiber_dir, int& id, double& w ); + void GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer m_PeakImage , vnl_vector_fixed fiber_dir, int& id, double& w, double& peak_mag ); void CreatePeakSystem(); void CreateDiffSystem(); void CreateScalarSystem(); void GenerateOutputPeakImages(); void GenerateOutputDiffImages(); void GenerateOutputScalarImages(); std::vector< mitk::FiberBundle::Pointer > m_Tractograms; PeakImgType::Pointer m_PeakImage; VectorImgType::Pointer m_DiffImage; DoubleImgType::Pointer m_ScalarImage; UcharImgType::Pointer m_MaskImage; bool m_FitIndividualFibers; double m_GradientTolerance; double m_Lambda; int m_MaxIterations; float m_FiberSampling; double m_Coverage; double m_Overshoot; double m_RMSE; bool m_FilterOutliers; double m_MeanWeight; double m_MedianWeight; double m_MinWeight; double m_MaxWeight; bool m_Verbose; bool m_DeepCopy; bool m_ResampleFibers; unsigned int m_NumUnknowns; unsigned int m_NumResiduals; unsigned int m_NumCoveredDirections; // output vnl_vector m_RmsDiffPerBundle; vnl_vector m_Weights; PeakImgType::Pointer m_UnderexplainedImage; PeakImgType::Pointer m_OverexplainedImage; PeakImgType::Pointer m_ResidualImage; PeakImgType::Pointer m_FittedImage; VectorImgType::Pointer m_UnderexplainedImageDiff; VectorImgType::Pointer m_OverexplainedImageDiff; VectorImgType::Pointer m_ResidualImageDiff; VectorImgType::Pointer m_FittedImageDiff; DoubleImgType::Pointer m_UnderexplainedImageScalar; DoubleImgType::Pointer m_OverexplainedImageScalar; DoubleImgType::Pointer m_ResidualImageScalar; DoubleImgType::Pointer m_FittedImageScalar; mitk::DiffusionSignalModel<>* m_SignalModel; vnl_sparse_matrix A; vnl_vector b; VnlCostFunction cost; int sz_x; int sz_y; int sz_z; int dim_four_size; double m_MeanTractDensity; double m_MeanSignal; unsigned int fiber_count; VnlCostFunction::REGU m_Regularization; std::vector m_GroupSizes; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkFitFibersToImageFilter.cpp" #endif #endif // __itkFitFibersToImageFilter_h__ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp index 8413aa80d9..ff59729c46 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp @@ -1,265 +1,266 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include "QmitkFiberFitView.h" #include #include #include #include #include #include #include #include #include #include #include #include +#include const std::string QmitkFiberFitView::VIEW_ID = "org.mitk.views.fiberfit"; using namespace mitk; QmitkFiberFitView::QmitkFiberFitView() : QmitkAbstractView() , m_Controls( nullptr ) { } // Destructor QmitkFiberFitView::~QmitkFiberFitView() { } void QmitkFiberFitView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberFitViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartFit()) ); connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3); m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractBox->SetPredicate(isFib); m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); - m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateAnd::New(isImage, is3D) ); + m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(isImage, is3D), mitk::TNodePredicateDataType::New()) ); DataSelectionChanged(); } } void QmitkFiberFitView::DataSelectionChanged() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) m_Controls->m_StartButton->setEnabled(false); else m_Controls->m_StartButton->setEnabled(true); } void QmitkFiberFitView::SetFocus() { DataSelectionChanged(); } void QmitkFiberFitView::StartFit() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) return; mitk::FiberBundle::Pointer input_tracts = dynamic_cast(m_Controls->m_TractBox->GetSelectedNode()->GetData()); mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData()); mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast(node->GetData()); if (mitk_peak_image.IsNotNull()) { typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitk_peak_image); caster->Update(); mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput(); fitter->SetPeakImage(peak_image); } else { if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image)); mitk::TensorModel<>* model = new mitk::TensorModel<>(); model->SetBvalue(1000); model->SetDiffusivity1(0.0010); model->SetDiffusivity2(0.00015); model->SetDiffusivity3(0.00015); model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image)); fitter->SetSignalModel(model); } else { itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New(); mitk::CastToItkImage(mitk_image, scalar_image); fitter->SetScalarImage(scalar_image); } } if (m_Controls->m_ReguTypeBox->currentIndex()==0) fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==1) fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==2) fitter->SetRegularization(VnlCostFunction::REGU::MSM); else if (m_Controls->m_ReguTypeBox->currentIndex()==3) fitter->SetRegularization(VnlCostFunction::REGU::LASSO); else if (m_Controls->m_ReguTypeBox->currentIndex()==4) fitter->SetRegularization(VnlCostFunction::REGU::NONE); fitter->SetTractograms({input_tracts}); fitter->SetFitIndividualFibers(true); fitter->SetMaxIterations(20); fitter->SetVerbose(true); fitter->SetGradientTolerance(1e-5); fitter->SetLambda(m_Controls->m_ReguBox->value()); fitter->SetFilterOutliers(m_Controls->m_OutliersBox->isChecked()); fitter->Update(); mitk::FiberBundle::Pointer output_tracts = fitter->GetTractograms().at(0); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(output_tracts); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); m_Controls->m_TractBox->GetSelectedNode()->SetVisibility(false); if (m_Controls->m_ResidualsBox->isChecked() && mitk_peak_image.IsNotNull()) { { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetFittedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetResidualImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetUnderexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Underexplained"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetOverexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Overexplained"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked()) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } } void QmitkFiberFitView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { }