diff --git a/Modules/MriSimulation/Algorithms/itkFitFibersToImageFilter.cpp b/Modules/MriSimulation/Algorithms/itkFitFibersToImageFilter.cpp
index 011eeb3..05d6bd8 100644
--- a/Modules/MriSimulation/Algorithms/itkFitFibersToImageFilter.cpp
+++ b/Modules/MriSimulation/Algorithms/itkFitFibersToImageFilter.cpp
@@ -1,985 +1,993 @@
 #include "itkFitFibersToImageFilter.h"
 
 #include <boost/progress.hpp>
 #include <mitkDiffusionFunctionCollection.h>
 
 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(1.0)
   , m_MaxIterations(20)
   , 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_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;
 
   if (m_MaskImage.IsNotNull() &&
       (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x ||
        m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y ||
        m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z))
     mitkThrow() << "Mask and peak image must have same size!";
 
   auto spacing = m_DiffImage->GetSpacing();
 
   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<int> voxel_indicator; voxel_indicator.set_size(sz_x*sz_y*sz_z); voxel_indicator.fill(0);
 
   unsigned int numFibers = 0;
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
     numFibers += m_Tractograms.at(bundle)->GetNumFibers();
   boost::progress_display disp(numFibers);
   m_GroupSizes.clear();
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
   {
     vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
     m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
     for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
     {
       ++disp;
       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; j<numPoints-1; ++j)
       {
         PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
         itk::Index<3> startIndex;
         itk::ContinuousIndex<float, 3> startIndexCont;
         m_DiffImage->TransformPhysicalPointToIndex(startVertex, startIndex);
         m_DiffImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
 
         PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
         itk::Index<3> endIndex;
         itk::ContinuousIndex<float, 3> endIndexCont;
         m_DiffImage->TransformPhysicalPointToIndex(endVertex, endIndex);
         m_DiffImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
 
         mitk::DiffusionSignalModel<>::GradientType fiber_dir;
         fiber_dir[0] = endVertex[0]-startVertex[0];
         fiber_dir[1] = endVertex[1]-startVertex[1];
         fiber_dir[2] = endVertex[2]-startVertex[2];
         fiber_dir.Normalize();
 
         std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
         for (std::pair< itk::Index<3>, double > seg : segments)
         {
           if (!m_DiffImage->GetLargestPossibleRegion().IsInside(seg.first) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0))
             continue;
 
           int x = seg.first[0];
           int y = seg.first[1];
           int z = seg.first[2];
 
           mitk::DiffusionSignalModel<>::PixelType simulated_pixel = m_SignalModel->SimulateMeasurement(fiber_dir)*seg.second;
           VectorImgType::PixelType measured_pixel = m_DiffImage->GetPixel(seg.first);
 
           double simulated_mean = 0;
           double measured_mean = 0;
           int num_nonzero_g = 0;
           for (int g=0; g<dim_four_size; ++g)
           {
             if( m_SignalModel->GetGradientDirection(g).GetNorm()<mitk::eps )
               continue;
             simulated_mean += simulated_pixel[g];
             measured_mean += (double)measured_pixel[g];
             ++num_nonzero_g;
           }
           simulated_mean /= num_nonzero_g;
           measured_mean /= num_nonzero_g;
           simulated_pixel -= simulated_mean;
 
           if (voxel_indicator[x + sz_x*y + sz_x*sz_y*z]==0)
             m_MeanSignal += measured_mean;
           m_MeanTractDensity += simulated_mean;
           voxel_indicator[x + sz_x*y + sz_x*sz_y*z] = 1;
 
           for (int g=0; g<dim_four_size; ++g)
           {
             unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z + sz_x*sz_y*sz_z*g;
 
             if (m_FitIndividualFibers)
             {
               b[linear_index] = (double)measured_pixel[g] - measured_mean;
               A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + simulated_pixel[g]);
             }
             else
             {
               b[linear_index] = (double)measured_pixel[g] - measured_mean;
               A.put(linear_index, bundle, A.get(linear_index, bundle) + simulated_pixel[g]);
             }
           }
         }
 
       }
 
       ++fiber_count;
     }
   }
 
   m_NumCoveredDirections = voxel_indicator.sum();
+  if (m_NumCoveredDirections==0 || m_MeanSignal<0.0001)
+    mitkThrow() << "No overlap between fibers and non-zero image!";
   m_MeanTractDensity /= m_NumCoveredDirections;
   m_MeanSignal /= m_NumCoveredDirections;
   b /= m_MeanSignal;
   b *= m_MeanTractDensity;
 }
 
 void FitFibersToImageFilter::CreatePeakSystem()
 {
   sz_x = m_PeakImage->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;
 
   itk::Vector< double, 3 > spacing;
   spacing[0] = m_PeakImage->GetSpacing()[0];
   spacing[1] = m_PeakImage->GetSpacing()[1];
   spacing[2] = m_PeakImage->GetSpacing()[2];
 
   PointType3 origin;
   origin[0] = m_PeakImage->GetOrigin()[0];
   origin[1] = m_PeakImage->GetOrigin()[1];
   origin[2] = m_PeakImage->GetOrigin()[2];
 
   UcharImgType::RegionType::SizeType size;
   size[0] = m_PeakImage->GetLargestPossibleRegion().GetSize()[0];
   size[1] = m_PeakImage->GetLargestPossibleRegion().GetSize()[1];
   size[2] = m_PeakImage->GetLargestPossibleRegion().GetSize()[2];
   UcharImgType::RegionType imageRegion; imageRegion.SetSize(size);
 
   itk::Matrix<double, 3, 3> direction;
   for (int r=0; r<3; r++)
     for (int c=0; c<3; c++)
       direction[r][c] = m_PeakImage->GetDirection()[r][c];
 
   if (m_MaskImage.IsNull())
   {
     m_MaskImage = UcharImgType::New();
     m_MaskImage->SetSpacing( spacing );
     m_MaskImage->SetOrigin( origin );
     m_MaskImage->SetDirection( direction );
     m_MaskImage->SetRegions( imageRegion );
     m_MaskImage->Allocate();
     m_MaskImage->FillBuffer(1);
   }
   else if (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x ||
            m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y ||
            m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z)
     mitkThrow() << "Mask and peak image must have same size!";
 
 
   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();
 
   int numFibers = 0;
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
     numFibers += m_Tractograms.at(bundle)->GetNumFibers();
   boost::progress_display disp(numFibers);
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
   {
     vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
 
     m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
     for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
     {
       ++disp;
       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; j<numPoints-1; ++j)
       {
         PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
         itk::Index<3> startIndex;
         itk::ContinuousIndex<float, 3> startIndexCont;
         m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex);
         m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
 
         PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
         itk::Index<3> endIndex;
         itk::ContinuousIndex<float, 3> endIndexCont;
         m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex);
         m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
 
         vnl_vector_fixed<float,3> fiber_dir;
         fiber_dir[0] = endVertex[0]-startVertex[0];
         fiber_dir[1] = endVertex[1]-startVertex[1];
         fiber_dir[2] = endVertex[2]-startVertex[2];
         fiber_dir.normalize();
 
         std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
         for (std::pair< itk::Index<3>, double > seg : segments)
         {
           if (!m_MaskImage->GetLargestPossibleRegion().IsInside(seg.first) || m_MaskImage->GetPixel(seg.first)==0)
             continue;
 
           itk::Index<4> idx4;
           idx4[0]=seg.first[0];
           idx4[1]=seg.first[1];
           idx4[2]=seg.first[2];
           idx4[3]=0;
 
           double w = 1;
           int peak_id = dim_four_size-1;
 
           double peak_mag = 0;
           GetClosestPeak(idx4, m_PeakImage, fiber_dir, peak_id, w, peak_mag);
           w *= seg.second;
 
           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_id<dim_four_size-1)
           {
             m_NumCoveredDirections++;
             m_MeanSignal += peak_mag;
           }
           m_MeanTractDensity += w;
 
           if (m_FitIndividualFibers)
           {
             b[linear_index] = peak_mag;
             A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + w);
           }
           else
           {
             b[linear_index] = peak_mag;
             A.put(linear_index, bundle, A.get(linear_index, bundle) + w);
           }
         }
       }
 
       ++fiber_count;
     }
   }
 
+  if (m_NumCoveredDirections==0 || m_MeanSignal<0.0001)
+    mitkThrow() << "No overlap between fibers and non-zero image!";
+
   m_MeanTractDensity /= m_NumCoveredDirections;
   m_MeanSignal /= m_NumCoveredDirections;
   b /= m_MeanSignal;
   b *= m_MeanTractDensity;
 }
 
 void FitFibersToImageFilter::CreateScalarSystem()
 {
   sz_x = m_ScalarImage->GetLargestPossibleRegion().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;
 
   if (m_MaskImage.IsNotNull() &&
       (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x ||
        m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y ||
        m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z))
     mitkThrow() << "Mask and peak image must have same size!";
 
   auto spacing = m_ScalarImage->GetSpacing();
   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;
 
   int numFibers = 0;
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
     numFibers += m_Tractograms.at(bundle)->GetNumFibers();
   boost::progress_display disp(numFibers);
   m_GroupSizes.clear();
   for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
   {
     vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
 
     m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
     for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
     {
       ++disp;
       vtkCell* cell = polydata->GetCell(i);
       int numPoints = cell->GetNumberOfPoints();
       vtkPoints* points = cell->GetPoints();
 
       for (int j=0; j<numPoints-1; ++j)
       {
         PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
         itk::Index<3> startIndex;
         itk::ContinuousIndex<float, 3> startIndexCont;
         m_ScalarImage->TransformPhysicalPointToIndex(startVertex, startIndex);
         m_ScalarImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
 
         PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
         itk::Index<3> endIndex;
         itk::ContinuousIndex<float, 3> endIndexCont;
         m_ScalarImage->TransformPhysicalPointToIndex(endVertex, endIndex);
         m_ScalarImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
 
         std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
         for (std::pair< itk::Index<3>, double > seg : segments)
         {
           if (!m_ScalarImage->GetLargestPossibleRegion().IsInside(seg.first) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0))
             continue;
 
           float image_value = m_ScalarImage->GetPixel(seg.first);
           int x = seg.first[0];
           int y = seg.first[1];
           int z = seg.first[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 += seg.second;
 
           if (m_FitIndividualFibers)
           {
             b[linear_index] = image_value;
             A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + seg.second);
           }
           else
           {
             b[linear_index] = image_value;
             A.put(linear_index, bundle, A.get(linear_index, bundle) + seg.second);
           }
         }
       }
 
       ++fiber_count;
     }
   }
 
+  if (numCoveredVoxels==0 || m_MeanSignal<0.0001)
+    mitkThrow() << "No overlap between fibers and non-zero image!";
+
   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; bundle<m_Tractograms.size(); bundle++)
       m_NumUnknowns += m_Tractograms.at(bundle)->GetNumFibers();
   }
   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!";
 
   MITK_INFO << "Initializing optimizer";
   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<double> l; l.set_size(m_NumUnknowns); l.fill(0);
   vnl_vector<long> 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);
 
   if (m_Regularization==VnlCostFunction::REGU::MSM)
     MITK_INFO << "Regularization type: MSM";
   else if (m_Regularization==VnlCostFunction::REGU::VARIANCE)
     MITK_INFO << "Regularization type: VARIANCE";
   else if (m_Regularization==VnlCostFunction::REGU::LASSO)
     MITK_INFO << "Regularization type: LASSO";
   else if (m_Regularization==VnlCostFunction::REGU::VOXEL_VARIANCE)
     MITK_INFO << "Regularization type: VOXEL_VARIANCE";
   else if (m_Regularization==VnlCostFunction::REGU::GROUP_LASSO)
     MITK_INFO << "Regularization type: GROUP_LASSO";
   else if (m_Regularization==VnlCostFunction::REGU::GROUP_VARIANCE)
     MITK_INFO << "Regularization type: GROUP_VARIANCE";
   else if (m_Regularization==VnlCostFunction::REGU::NONE)
     MITK_INFO << "Regularization type: NONE";
 
 //  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<double> dx; dx.set_size(m_NumUnknowns); dx.fill(0.0);
 //    cost.calc_regularization_gradient(m_Weights, dx);
 
 //    if (m_Weights.magnitude()==0)
 //    {
 //      MITK_INFO << "Regularization estimation failed. Using default value.";
 //      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;
 //      }
 //    }
 //  }
 //  else
 //    cost.m_Lambda = 0;
   cost.m_Lambda = 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<double> 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 RMSE: " << 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<m_Tractograms.size(); bundle++)
     {
       vnl_vector< double > temp_weights;
       temp_weights.set_size(m_Weights.size());
       temp_weights.copy_in(m_Weights.data_block());
 
       for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); 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;
     }
   }
   else
   {
     for (unsigned int i=0; i<m_Tractograms.size(); ++i)
     {
       vnl_vector< double > 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]);
     }
   }
   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<double> fitted_b; fitted_b.set_size(b.size());
   cost.S->multiply(m_Weights, fitted_b);
 
   itk::ImageRegionIterator<VectorImgType> it1 = itk::ImageRegionIterator<VectorImgType>(m_DiffImage, m_DiffImage->GetLargestPossibleRegion());
   itk::ImageRegionIterator<VectorImgType> it2 = itk::ImageRegionIterator<VectorImgType>(m_FittedImageDiff, m_FittedImageDiff->GetLargestPossibleRegion());
   itk::ImageRegionIterator<VectorImgType> it3 = itk::ImageRegionIterator<VectorImgType>(m_ResidualImageDiff, m_ResidualImageDiff->GetLargestPossibleRegion());
   itk::ImageRegionIterator<VectorImgType> it4 = itk::ImageRegionIterator<VectorImgType>(m_UnderexplainedImageDiff, m_UnderexplainedImageDiff->GetLargestPossibleRegion());
   itk::ImageRegionIterator<VectorImgType> it5 = itk::ImageRegionIterator<VectorImgType>(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; g<dim_four_size; ++g)
     {
       if( m_SignalModel->GetGradientDirection(g).GetNorm()>=mitk::eps )
       {
         original_mean += original_pix[g];
         ++num_nonzero_g;
       }
     }
     original_mean /= num_nonzero_g;
 
     for (int g=0; g<dim_four_size; ++g)
     {
       unsigned int linear_index = idx3[0] + sz_x*idx3[1] + sz_x*sz_y*idx3[2] + sz_x*sz_y*sz_z*g;
 
       fitted_pix[g] = fitted_b[linear_index] + original_mean;
       residual_pix[g] = original_pix[g] - fitted_b[linear_index] - original_mean;
 
       if (residual_pix[g]<0)
       {
         overexplained_pix[g] = residual_pix[g];
         m_Coverage += b[linear_index] + original_mean;
         m_Overshoot -= residual_pix[g];
       }
       else if (residual_pix[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<double> fitted_b; fitted_b.set_size(b.size());
   cost.S->multiply(m_Weights, fitted_b);
 
   itk::ImageRegionIterator<DoubleImgType> it1 = itk::ImageRegionIterator<DoubleImgType>(m_ScalarImage, m_ScalarImage->GetLargestPossibleRegion());
   itk::ImageRegionIterator<DoubleImgType> it2 = itk::ImageRegionIterator<DoubleImgType>(m_FittedImageScalar, m_FittedImageScalar->GetLargestPossibleRegion());
   itk::ImageRegionIterator<DoubleImgType> it3 = itk::ImageRegionIterator<DoubleImgType>(m_ResidualImageScalar, m_ResidualImageScalar->GetLargestPossibleRegion());
   itk::ImageRegionIterator<DoubleImgType> it4 = itk::ImageRegionIterator<DoubleImgType>(m_UnderexplainedImageScalar, m_UnderexplainedImageScalar->GetLargestPossibleRegion());
   itk::ImageRegionIterator<DoubleImgType> it5 = itk::ImageRegionIterator<DoubleImgType>(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<double> fitted_b; fitted_b.set_size(b.size());
   cost.S->multiply(m_Weights, fitted_b);
 
   for (unsigned int r=0; r<b.size(); r++)
   {
     itk::Index<4> 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<dim_four_size-1)
     {
       vnl_vector_fixed<float,3> 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]<sz_x; ++idx4[0])
     for (idx4[1]=0; idx4[1]<sz_y; ++idx4[1])
       for (idx4[2]=0; idx4[2]<sz_z; ++idx4[2])
       {
         itk::Index<3> 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<float,3> peak_dir;
         vnl_vector_fixed<float,3> fitted_dir;
         vnl_vector_fixed<float,3> 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]);
             }
           }
         }
       }
 }
 
 void FitFibersToImageFilter::GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed<float,3> fiber_dir, int& id, double& w, double& peak_mag )
 {
   int m_NumDirs = peak_image->GetLargestPossibleRegion().GetSize()[3]/3;
   vnl_vector_fixed<float,3> out_dir; out_dir.fill(0);
   float angle = 0.9;
 
   for (int i=0; i<m_NumDirs; i++)
   {
     vnl_vector_fixed<float,3> 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 (mag<mitk::eps)
       continue;
 
     float a = fabs(dot_product(dir, fiber_dir))/mag;
     if (a>angle)
     {
       angle = a;
       w = angle;
       peak_mag = mag;
       id = i;
     }
   }
 }
 
 std::vector<mitk::FiberBundle::Pointer> FitFibersToImageFilter::GetTractograms() const
 {
   return m_Tractograms;
 }
 
 void FitFibersToImageFilter::SetTractograms(const std::vector<mitk::FiberBundle::Pointer> &tractograms)
 {
   m_Tractograms = tractograms;
 }
 
 void FitFibersToImageFilter::SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel)
 {
   m_SignalModel = SignalModel;
 }
 
 }