diff --git a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
index 0059159..2b52d5a 100644
--- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
+++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
@@ -1,2849 +1,2849 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center.
 
 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 "mitkFiberBundle.h"
 
 #include <mitkPlanarCircle.h>
 #include <mitkPlanarPolygon.h>
 #include <mitkPlanarFigureComposite.h>
 #include <mitkDiffusionFunctionCollection.h>
 #include <mitkPixelTypeMultiplex.h>
 
 #include <vtkPointData.h>
 #include <vtkDataArray.h>
 #include <vtkUnsignedCharArray.h>
 #include <vtkPolyLine.h>
 #include <vtkCellArray.h>
 #include <vtkCellData.h>
 #include <vtkIdFilter.h>
 #include <vtkClipPolyData.h>
 #include <vtkPlane.h>
 #include <vtkDoubleArray.h>
 #include <vtkKochanekSpline.h>
 #include <vtkParametricFunctionSource.h>
 #include <vtkParametricSpline.h>
 #include <vtkPolygon.h>
 #include <vtkCleanPolyData.h>
 #include <boost/timer/progress_display.hpp>
 #include <vtkTransformPolyDataFilter.h>
 #include <mitkTransferFunction.h>
 #include <vtkLookupTable.h>
 #include <mitkLookupTable.h>
 #include <vtkCardinalSpline.h>
 #include <vtkAppendPolyData.h>
 #include <random>
 #include <algorithm>
 
 
 const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs";
 
 mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData )
   : m_NumFibers(0)
 {
   m_TrackVisHeader.hdr_size = 0;
   m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
   m_FiberWeights->SetName("FIBER_WEIGHTS");
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   if (fiberPolyData != nullptr)
     m_FiberPolyData = fiberPolyData;
   else
   {
     this->m_FiberPolyData->SetPoints(vtkSmartPointer<vtkPoints>::New());
     this->m_FiberPolyData->SetLines(vtkSmartPointer<vtkCellArray>::New());
   }
 
   this->UpdateFiberGeometry();
   this->GenerateFiberIds();
   this->ColorFibersByOrientation();
 }
 
 mitk::FiberBundle::~FiberBundle()
 {
 
 }
 
 mitk::FiberBundle::Pointer mitk::FiberBundle::GetDeepCopy()
 {
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(m_FiberPolyData);
   newFib->SetFiberColors(this->m_FiberColors);
   newFib->SetFiberWeights(this->m_FiberWeights);
   newFib->SetTrackVisHeader(this->GetTrackVisHeader());
   return newFib;
 }
 
 vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights)
 {
   vtkSmartPointer<vtkPolyData> newFiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> newLineSet = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> newPointSet = vtkSmartPointer<vtkPoints>::New();
   weights->SetNumberOfValues(fiberIds.size());
 
   int counter = 0;
   auto finIt = fiberIds.begin();
   while ( finIt != fiberIds.end() )
   {
     if (*finIt>GetNumFibers()){
       MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt;
       break;
     }
 
     vtkSmartPointer<vtkCell> fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber);
     vtkSmartPointer<vtkPoints> fibPoints = fiber->GetPoints();
     vtkSmartPointer<vtkPolyLine> newFiber = vtkSmartPointer<vtkPolyLine>::New();
     newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() );
 
     for(int i=0; i<fibPoints->GetNumberOfPoints(); i++)
     {
       newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints());
       newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]);
     }
 
     weights->InsertValue(counter, this->GetFiberWeight(*finIt));
     newLineSet->InsertNextCell(newFiber);
     ++finIt;
     ++counter;
   }
 
   newFiberPolyData->SetPoints(newPointSet);
   newFiberPolyData->SetLines(newLineSet);
   return newFiberPolyData;
 }
 
 // merge two fiber bundles
 mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs)
 {
   vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
   // add current fiber bundle
   vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
 
   auto num_weights = this->GetNumFibers();
   for (auto fib : fibs)
     num_weights += fib->GetNumFibers();
   weights->SetNumberOfValues(num_weights);
 
   unsigned int counter = 0;
   for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); ++i)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (unsigned int j=0; j<numPoints; ++j)
     {
       double p[3];
       points->GetPoint(j, p);
 
       vtkIdType id = vNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     weights->InsertValue(counter, this->GetFiberWeight(i));
     vNewLines->InsertNextCell(container);
     counter++;
   }
 
   for (auto fib : fibs)
   {
     // add new fiber bundle
     for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
     {
       vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
       auto numPoints = cell->GetNumberOfPoints();
       vtkPoints* points = cell->GetPoints();
 
       vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
       for (unsigned int j=0; j<numPoints; j++)
       {
         double p[3];
         points->GetPoint(j, p);
 
         vtkIdType id = vNewPoints->InsertNextPoint(p);
         container->GetPointIds()->InsertNextId(id);
       }
       weights->InsertValue(counter, fib->GetFiberWeight(i));
       vNewLines->InsertNextCell(container);
       counter++;
     }
   }
 
   // initialize PolyData
   vNewPolyData->SetPoints(vNewPoints);
   vNewPolyData->SetLines(vNewLines);
 
   // initialize fiber bundle
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
   newFib->SetFiberWeights(weights);
   return newFib;
 }
 
 // merge two fiber bundles
 mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundle(mitk::FiberBundle* fib)
 {
   if (fib==nullptr)
     return this->GetDeepCopy();
 
   MITK_INFO << "Adding fibers";
 
   vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
   // add current fiber bundle
   vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
   weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers());
 
   unsigned int counter = 0;
   for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (unsigned int j=0; j<numPoints; j++)
     {
       double p[3];
       points->GetPoint(j, p);
 
       vtkIdType id = vNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     weights->InsertValue(counter, this->GetFiberWeight(i));
     vNewLines->InsertNextCell(container);
     counter++;
   }
 
   // add new fiber bundle
   for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
   {
     vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (unsigned int j=0; j<numPoints; j++)
     {
       double p[3];
       points->GetPoint(j, p);
 
       vtkIdType id = vNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     weights->InsertValue(counter, fib->GetFiberWeight(i));
     vNewLines->InsertNextCell(container);
     counter++;
   }
 
   // initialize PolyData
   vNewPolyData->SetPoints(vNewPoints);
   vNewPolyData->SetLines(vNewLines);
 
   // initialize fiber bundle
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
   newFib->SetFiberWeights(weights);
   return newFib;
 }
 
 // Only retain fibers with a weight larger than the specified threshold
 mitk::FiberBundle::Pointer mitk::FiberBundle::FilterByWeights(float weight_thr, bool invert)
 {
   vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
   std::vector<float> weights;
 
   for (unsigned int i=0; i<this->GetNumFibers(); i++)
   {
     if ( (invert && this->GetFiberWeight(i)>weight_thr) || (!invert && this->GetFiberWeight(i)<=weight_thr))
       continue;
 
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double p[3];
       points->GetPoint(j, p);
 
       vtkIdType id = vNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     vNewLines->InsertNextCell(container);
     weights.push_back(this->GetFiberWeight(i));
   }
 
   // initialize PolyData
   vNewPolyData->SetPoints(vNewPoints);
   vNewPolyData->SetLines(vNewLines);
 
   // initialize fiber bundle
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
   for (unsigned int i=0; i<weights.size(); ++i)
     newFib->SetFiberWeight(i, weights.at(i));
   newFib->SetTrackVisHeader(this->GetTrackVisHeader());
   return newFib;
 }
 
 // Only retain a subsample of the fibers
 mitk::FiberBundle::Pointer mitk::FiberBundle::SubsampleFibers(float factor, bool random_seed)
 {
   vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
   unsigned int new_num_fibs = static_cast<unsigned int>(std::round(this->GetNumFibers()*factor));
   MITK_INFO << "Subsampling fibers with factor " << factor << "(" << new_num_fibs << "/" << this->GetNumFibers() << ")";
 
   // add current fiber bundle
   vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
   weights->SetNumberOfValues(new_num_fibs);
 
   std::vector< unsigned int > ids;
   for (unsigned int i=0; i<this->GetNumFibers(); i++)
     ids.push_back(i);
   if (random_seed)
     std::srand(static_cast<unsigned int>(std::time(nullptr)));
   else
     std::srand(0);
 	
   std::random_device rd;
   std::mt19937 g(rd());
   std::shuffle(ids.begin(), ids.end(), g);
 
   unsigned int counter = 0;
   for (unsigned int i=0; i<new_num_fibs; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(ids.at(i));
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double p[3];
       points->GetPoint(j, p);
 
       vtkIdType id = vNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     weights->InsertValue(counter, this->GetFiberWeight(ids.at(i)));
     vNewLines->InsertNextCell(container);
     counter++;
   }
 
   // initialize PolyData
   vNewPolyData->SetPoints(vNewPoints);
   vNewPolyData->SetLines(vNewLines);
 
   // initialize fiber bundle
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
   newFib->SetFiberWeights(weights);
   newFib->SetTrackVisHeader(this->GetTrackVisHeader());
   return newFib;
 }
 
 // subtract two fiber bundles
 mitk::FiberBundle::Pointer mitk::FiberBundle::SubtractBundle(mitk::FiberBundle* fib)
 {
   if (fib==nullptr)
     return this->GetDeepCopy();
 
   MITK_INFO << "Subtracting fibers";
   vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
   vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
   std::vector< std::vector< itk::Point<float, 3> > > points1;
   for(unsigned int i=0; i<m_NumFibers; i++ )
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     if (points==nullptr || numPoints<=0)
       continue;
 
     itk::Point<float, 3> start = mitk::imv::GetItkPoint(points->GetPoint(0));
     itk::Point<float, 3> end = mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
 
     points1.push_back( {start, end} );
   }
 
   std::vector< std::vector< itk::Point<float, 3> > > points2;
   for(unsigned int i=0; i<fib->GetNumFibers(); i++ )
   {
     vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     if (points==nullptr || numPoints<=0)
       continue;
 
     itk::Point<float, 3> start =mitk::imv::GetItkPoint(points->GetPoint(0));
     itk::Point<float, 3> end =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
 
     points2.push_back( {start, end} );
   }
 
   //  int progress = 0;
   std::vector< int > ids;
 #pragma omp parallel for
   for (int i=0; i<static_cast<int>(points1.size()); i++)
   {
     bool match = false;
     for (unsigned int j=0; j<points2.size(); j++)
     {
       auto v1 = points1.at(static_cast<unsigned int>(i));
       auto v2 = points2.at(j);
 
       float dist=0;
       for (unsigned int c=0; c<v1.size(); c++)
       {
         float d = v1[c][0]-v2[c][0];
         dist += d*d;
 
         d = v1[c][1]-v2[c][1];
         dist += d*d;
 
         d = v1[c][2]-v2[c][2];
         dist += d*d;
       }
       dist /= v1.size();
 
       if (dist<0.000001f)
       {
         match = true;
         break;
       }
 
       dist=0;
       for (unsigned int c=0; c<v1.size(); c++)
       {
         float d = v1[v1.size()-1-c][0]-v2[c][0];
         dist += d*d;
 
         d = v1[v1.size()-1-c][1]-v2[c][1];
         dist += d*d;
 
         d = v1[v1.size()-1-c][2]-v2[c][2];
         dist += d*d;
       }
       dist /= v1.size();
 
       if (dist<0.000001f)
       {
         match = true;
         break;
       }
     }
 
 #pragma omp critical
     if (!match)
       ids.push_back(i);
   }
 
   for( int i : ids )
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     if (points==nullptr || numPoints<=0)
       continue;
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for( int j=0; j<numPoints; j++)
     {
       vtkIdType id = vNewPoints->InsertNextPoint(points->GetPoint(j));
       container->GetPointIds()->InsertNextId(id);
     }
     vNewLines->InsertNextCell(container);
   }
   if(vNewLines->GetNumberOfCells()==0)
     return mitk::FiberBundle::New();
   // initialize PolyData
   vNewPolyData->SetPoints(vNewPoints);
   vNewPolyData->SetLines(vNewLines);
 
   // initialize fiber bundle
   return mitk::FiberBundle::New(vNewPolyData);
 }
 
 /*
  * set PolyData (additional flag to recompute fiber geometry, default = true)
  */
 void mitk::FiberBundle::SetFiberPolyData(vtkSmartPointer<vtkPolyData> fiberPD, bool updateGeometry)
 {
   if (fiberPD == nullptr)
     this->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   else
   {
     m_FiberPolyData->CopyStructure(fiberPD);
 //    m_FiberPolyData->DeepCopy(fiberPD);
   }
 
   m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfLines());
 
   if (updateGeometry)
     UpdateFiberGeometry();
   GenerateFiberIds();
   ColorFibersByOrientation();
 }
 
 /*
  * return vtkPolyData
  */
 vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GetFiberPolyData() const
 {
   return m_FiberPolyData;
 }
 
 void mitk::FiberBundle::ColorFibersByLength(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type)
 {
   if (m_MaxFiberLength<=0)
     return;
 
   auto numOfPoints = this->GetNumberOfPoints();
 
   //colors and alpha value for each single point, RGBA = 4 components
   unsigned char rgba[4] = {0,0,0,0};
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(numOfPoints * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
   if (numOfFibers < 1)
     return;
 
   mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
   mitkLookup->SetType(type);
   if (type!=mitk::LookupTable::MULTILABEL)
     mitkLookup->GetVtkLookupTable()->SetTableRange(m_MinFiberLength, m_MaxFiberLength);
 
   unsigned int count = 0;
   for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
 
     float l = m_FiberLengths.at(i)/m_MaxFiberLength;
     double color[3];
     mitkLookup->GetColor(m_FiberLengths.at(i), color);
 
     for (int j=0; j<numPoints; j++)
     {
 
       rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
       rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
       rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
       if (opacity)
         rgba[3] = static_cast<unsigned char>(255.0f * l);
       else
         rgba[3] = static_cast<unsigned char>(255.0);
       m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
       count++;
     }
 
     if (weight_fibers)
       this->SetFiberWeight(i, m_FiberLengths.at(i));
   }
 
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::ColorSinglePoint(int f_idx, int p_idx, double rgb[3])
 {
 //  vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
 //  vtkIdType numOfPoints = 0;
 //  if (extrPoints!=nullptr)
 //    numOfPoints = extrPoints->GetNumberOfPoints();
 
 //  //colors and alpha value for each single point, RGBA = 4 components
   unsigned char rgba[4] = {0,0,0,0};
 //  m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
 //  m_FiberColors->Allocate(numOfPoints * 4);
 //  m_FiberColors->SetNumberOfComponents(4);
 //  m_FiberColors->SetName("FIBER_COLORS");
 
 //  auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
 //  if (numOfFibers < 1)
 //    return;
 
 //  /* extract single fibers of fiberBundle */
 //  vtkCellArray* fiberList = m_FiberPolyData->GetLines();
 //  fiberList->InitTraversal();
 
 //  for (int fi=0; fi<numOfFibers; ++fi)
 //  {
 
 //    vtkIdType* idList; // contains the point id's of the line
 //    vtkIdType num_points; // number of points for current line
 ////    fiberList->GetNextCell(num_points, idList);
 //    fiberList->GetCell(f_idx, num_points, idList);
 
     vtkCell* cell = m_FiberPolyData->GetCell(f_idx);
 
 
 //    /* single fiber checkpoints: is number of points valid */
 //    if (p_idx < num_points)
 //    {
       rgba[0] = static_cast<unsigned char>(255.0 * rgb[0]);
       rgba[1] = static_cast<unsigned char>(255.0 * rgb[1]);
       rgba[2] = static_cast<unsigned char>(255.0 * rgb[2]);
       rgba[3] = 255;
 
       m_FiberColors->InsertTypedTuple(cell->GetPointId(p_idx), rgba);
 //    }
 //  }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::ColorFibersByOrientation()
 {
   //===== FOR WRITING A TEST ========================
   //  colorT size == tupelComponents * tupelElements
   //  compare color results
   //  to cover this code 100% also PolyData needed, where colorarray already exists
   //  + one fiber with exactly 1 point
   //  + one fiber with 0 points
   //=================================================
 
   vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
   vtkIdType numOfPoints = 0;
   if (extrPoints!=nullptr)
     numOfPoints = extrPoints->GetNumberOfPoints();
 
   //colors and alpha value for each single point, RGBA = 4 components
   unsigned char rgba[4] = {0,0,0,0};
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(numOfPoints * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
   if (numOfFibers < 1)
     return;
 
   /* extract single fibers of fiberBundle */
   vtkCellArray* fiberList = m_FiberPolyData->GetLines();
   fiberList->InitTraversal();
   for (int fi=0; fi<numOfFibers; ++fi) {
 
     vtkIdType const* idList; // contains the point id's of the line
     vtkIdType pointsPerFiber; // number of points for current line
     fiberList->GetNextCell(pointsPerFiber, idList);
 
     /* single fiber checkpoints: is number of points valid */
     if (pointsPerFiber > 1)
     {
       /* operate on points of single fiber */
       for (int i=0; i <pointsPerFiber; ++i)
       {
         /* process all points elastV[0]ept starting and endpoint for calculating color value take current point, previous point and next point */
         if (i<pointsPerFiber-1 && i > 0)
         {
           /* The color value of the current point is influenced by the previous point and next point. */
           vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
           vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
           vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
 
           vnl_vector_fixed< double, 3 > diff1;
           diff1 = currentPntvtk - nextPntvtk;
 
           vnl_vector_fixed< double, 3 > diff2;
           diff2 = currentPntvtk - prevPntvtk;
 
           vnl_vector_fixed< double, 3 > diff;
           diff = (diff1 - diff2) / 2.0;
           diff.normalize();
 
           rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff[0]));
           rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff[1]));
           rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff[2]));
           rgba[3] = static_cast<unsigned char>(255.0);
         }
         else if (i==0)
         {
           /* First point has no previous point, therefore only diff1 is taken */
 
           vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
           vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
 
           vnl_vector_fixed< double, 3 > diff1;
           diff1 = currentPntvtk - nextPntvtk;
           diff1.normalize();
 
           rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff1[0]));
           rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff1[1]));
           rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff1[2]));
           rgba[3] = static_cast<unsigned char>(255.0);
         }
         else if (i==pointsPerFiber-1)
         {
           /* Last point has no next point, therefore only diff2 is taken */
           vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
           vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
 
           vnl_vector_fixed< double, 3 > diff2;
           diff2 = currentPntvtk - prevPntvtk;
           diff2.normalize();
 
           rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff2[0]));
           rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff2[1]));
           rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff2[2]));
           rgba[3] = static_cast<unsigned char>(255.0);
         }
         m_FiberColors->InsertTypedTuple(idList[i], rgba);
       }
     }
     else if (pointsPerFiber == 1)
     {
       /* a single point does not define a fiber (use vertex mechanisms instead */
       continue;
     }
     else
     {
       MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ;
       continue;
     }
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::ColorFibersByCurvature(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type)
 {
   double window = 5;
 
   //colors and alpha value for each single point, RGBA = 4 components
   unsigned char rgba[4] = {0,0,0,0};
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   std::vector< double > values;
   double min = 1;
   double max = 0;
   MITK_INFO << "Coloring fibers by curvature";
   boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
 
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     ++disp;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
     double mean_curv = 0;
 
     // calculate curvatures
     for (int j=0; j<numPoints; j++)
     {
       double dist = 0;
       int c = j;
       std::vector< vnl_vector_fixed< double, 3 > > vectors;
       vnl_vector_fixed< double, 3 > meanV; meanV.fill(0.0);
       while(dist<window/2 && c>1)
       {
         double p1[3];
         points->GetPoint(c-1, p1);
         double p2[3];
         points->GetPoint(c, p2);
 
         vnl_vector_fixed< double, 3 > v;
         v[0] = p2[0]-p1[0];
         v[1] = p2[1]-p1[1];
         v[2] = p2[2]-p1[2];
         dist += v.magnitude();
         v.normalize();
         vectors.push_back(v);
         meanV += v;
         c--;
       }
       c = j;
       dist = 0;
       while(dist<window/2 && c<numPoints-1)
       {
         double p1[3];
         points->GetPoint(c, p1);
         double p2[3];
         points->GetPoint(c+1, p2);
 
         vnl_vector_fixed< double, 3 > v;
         v[0] = p2[0]-p1[0];
         v[1] = p2[1]-p1[1];
         v[2] = p2[2]-p1[2];
         dist += v.magnitude();
         v.normalize();
         vectors.push_back(v);
         meanV += v;
         c++;
       }
       meanV.normalize();
 
       double dev = 0;
       for (unsigned int c=0; c<vectors.size(); c++)
       {
         double angle = dot_product(meanV, vectors.at(c));
         if (angle>1.0)
           angle = 1.0;
         if (angle<-1.0)
           angle = -1.0;
         dev += acos(angle)*180/itk::Math::pi;
       }
       if (vectors.size()>0)
         dev /= vectors.size();
 
       if (weight_fibers)
         mean_curv += dev;
       dev = 1.0-dev/180.0;
       values.push_back(dev);
       if (dev<min)
         min = dev;
       if (dev>max)
         max = dev;
     }
 
     if (weight_fibers)
       this->SetFiberWeight(i, mean_curv/numPoints);
   }
 
   mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
   mitkLookup->SetType(type);
   if (type!=mitk::LookupTable::MULTILABEL)
     mitkLookup->GetVtkLookupTable()->SetTableRange(min, max);
 
   unsigned int count = 0;
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     for (int j=0; j<numPoints; j++)
     {
       double color[3];
       double dev = values.at(count);
       mitkLookup->GetColor(dev, color);
 
       rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
       rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
       rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
 
       if (opacity)
         rgba[3] = static_cast<unsigned char>(255.0f * dev/max);
       else
         rgba[3] = static_cast<unsigned char>(255.0);
 
       m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
       count++;
     }
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::SetFiberOpacity(vtkDoubleArray* FAValArray)
 {
   for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
   {
     double faValue = FAValArray->GetValue(i);
     faValue = faValue * 255.0;
     m_FiberColors->SetComponent(i,3, static_cast<unsigned char>(faValue) );
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::ResetFiberOpacity()
 {
   for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
     m_FiberColors->SetComponent(i,3, 255.0 );
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate)
 {
   if (FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned char" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="char" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="long" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned long" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="short" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned short" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned int" ||
            FAimage->GetPixelType().GetComponentTypeAsString()=="int")
   {
     typedef itk::Image<int, 3> ImageType;
     ImageType::Pointer itkImage = ImageType::New();
     CastToItkImage(FAimage, itkImage);
 
     ColorFibersByScalarMap<int>(itkImage, opacity, weight_fibers, type, max_cap, interpolate );
   }
   else
   {
     typedef itk::Image<float, 3> ImageType;
     ImageType::Pointer itkImage = ImageType::New();
     CastToItkImage(FAimage, itkImage);
 
     ColorFibersByScalarMap<float>(itkImage, opacity, weight_fibers, type, max_cap, interpolate );
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 template <typename TPixel>
-void mitk::FiberBundle::ColorFibersByScalarMap(typename itk::Image<TPixel, 3>::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate)
+void mitk::FiberBundle::ColorFibersByScalarMap(typename itk::Image<TPixel, 3>::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double , bool interpolate)
 {
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   unsigned char rgba[4] = {0,0,0,0};
   vtkPoints* pointSet = m_FiberPolyData->GetPoints();
 
   if (type==mitk::LookupTable::MULTILABEL)
     interpolate = false;
 
   auto interpolator = itk::LinearInterpolateImageFunction< itk::Image<TPixel, 3>, float >::New();
   interpolator->SetInputImage(image);
 
   double min = 999999;
   double max = -999999;
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
     double mean_val = 0;
 
     for (int j=0; j<numPoints; j++)
     {
       double p[3];
       points->GetPoint(j, p);
       auto pixelValue = mitk::imv::GetImageValue<TPixel>(mitk::imv::GetItkPoint(p), interpolate, interpolator);
 
       if (pixelValue>max)
         max = pixelValue;
       if (pixelValue<min)
         min = pixelValue;
 
       if (weight_fibers)
         mean_val += pixelValue;
     }
 
     if (weight_fibers)
       this->SetFiberWeight(i, mean_val/numPoints);
   }
 
   mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
   mitkLookup->SetType(type);
-  if (type!=mitk::LookupTable::MULTILABEL)
-    mitkLookup->GetVtkLookupTable()->SetTableRange(min, max*max_cap);
+//  if (type!=mitk::LookupTable::MULTILABEL)
+//    mitkLookup->GetVtkLookupTable()->SetTableRange(min, max*max_cap);
 
   for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
   {
     itk::Point<float, 3> px;
     px[0] = pointSet->GetPoint(i)[0];
     px[1] = pointSet->GetPoint(i)[1];
     px[2] = pointSet->GetPoint(i)[2];
     auto pixelValue = mitk::imv::GetImageValue<TPixel>(px, interpolate, interpolator);
 
     double color[3];
     mitkLookup->GetColor(pixelValue, color);
 
     rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
     rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
     rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
     if (opacity)
       rgba[3] = static_cast<unsigned char>(255.0 * pixelValue);
     else
       rgba[3] = static_cast<unsigned char>(255.0);
     m_FiberColors->InsertTypedTuple(i, rgba);
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 
 void mitk::FiberBundle::ColorFibersByFiberWeights(bool opacity, mitk::LookupTable::LookupTableType type)
 {
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   unsigned char rgba[4] = {0,0,0,0};
   unsigned int counter = 0;
 
   float max = -999999;
   float min = 999999;
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     float weight = this->GetFiberWeight(i);
     if (weight>max)
       max = weight;
     if (weight<min)
       min = weight;
   }
   if (fabs(max-min)<0.00001f)
   {
     max = 1;
     min = 0;
   }
 
   mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
   mitkLookup->SetType(type);
   if (type!=mitk::LookupTable::MULTILABEL)
     mitkLookup->GetVtkLookupTable()->SetTableRange(min, max);
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     auto weight = this->GetFiberWeight(i);
 
     double color[3];
     mitkLookup->GetColor(weight, color);
 
     for (int j=0; j<numPoints; j++)
     {
       rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
       rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
       rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
       if (opacity)
         rgba[3] = static_cast<unsigned char>(255.0f * weight/max);
       else
         rgba[3] = static_cast<unsigned char>(255.0);
 
       m_FiberColors->InsertTypedTuple(counter, rgba);
       counter++;
     }
   }
 
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::SetFiberColors(float r, float g, float b, float alpha)
 {
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   unsigned char rgba[4] = {0,0,0,0};
   for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
   {
     rgba[0] = static_cast<unsigned char>(r);
     rgba[1] = static_cast<unsigned char>(g);
     rgba[2] = static_cast<unsigned char>(b);
     rgba[3] = static_cast<unsigned char>(alpha);
     m_FiberColors->InsertTypedTuple(i, rgba);
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 void mitk::FiberBundle::GenerateFiberIds()
 {
   if (m_FiberPolyData == nullptr)
     return;
 
   vtkSmartPointer<vtkIdFilter> idFiberFilter = vtkSmartPointer<vtkIdFilter>::New();
   idFiberFilter->SetInputData(m_FiberPolyData);
   idFiberFilter->CellIdsOn();
   //  idFiberFilter->PointIdsOn(); // point id's are not needed
   idFiberFilter->SetCellIdsArrayName(FIBER_ID_ARRAY);
   idFiberFilter->FieldDataOn();
   idFiberFilter->Update();
 
   m_FiberIdDataSet = idFiberFilter->GetOutput();
 }
 
 float mitk::FiberBundle::GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label)
 {
   vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
 
   MITK_INFO << "Calculating EP-Fraction";
 
   boost::timer::progress_display disp(m_NumFibers);
   unsigned int in_mask = 0;
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = PolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(0));
     itk::Index<3> startIndex;
     mask->TransformPhysicalPointToIndex(startVertex, startIndex);
 
     itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
     itk::Index<3> endIndex;
     mask->TransformPhysicalPointToIndex(endVertex, endIndex);
 
     if (mask->GetLargestPossibleRegion().IsInside(startIndex) && mask->GetLargestPossibleRegion().IsInside(endIndex))
     {
       float v1 = mask->GetPixel(startIndex);
       if (v1 < 0.5f)
         continue;
       float v2 = mask->GetPixel(startIndex);
       if (v2 < 0.5f)
         continue;
 
       if (!different_label)
         ++in_mask;
       else if (fabs(v1-v2)>0.00001f)
         ++in_mask;
     }
   }
   return float(in_mask)/m_NumFibers;
 }
 
 std::tuple<float, float> mitk::FiberBundle::GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image)
 {
   vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
 
   MITK_INFO << "Calculating overlap";
   auto spacing = mask->GetSpacing();
   boost::timer::progress_display disp(m_NumFibers);
   double length_sum = 0;
   double in_mask_length = 0;
   double aligned_length = 0;
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = PolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     for (int j=0; j<numPoints-1; j++)
     {
       itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
       itk::Index<3> startIndex;
       itk::ContinuousIndex<float, 3> startIndexCont;
       mask->TransformPhysicalPointToIndex(startVertex, startIndex);
       mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
 
       itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
       itk::Index<3> endIndex;
       itk::ContinuousIndex<float, 3> endIndexCont;
       mask->TransformPhysicalPointToIndex(endVertex, endIndex);
       mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
       
       vnl_vector_fixed< float, 3 > fdir;
       fdir[0] = endVertex[0] - startVertex[0];
       fdir[1] = endVertex[1] - startVertex[1];
       fdir[2] = endVertex[2] - startVertex[2];
       fdir.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 > segment : segments)
       {
         if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
         {
           in_mask_length += segment.second;
           
           mitk::PeakImage::ItkPeakImageType::IndexType idx4; 
           idx4[0] = segment.first[0]; 
           idx4[1] = segment.first[1]; 
           idx4[2] = segment.first[2];
           
           vnl_vector_fixed< float, 3 > peak;
           idx4[3] = 0;
           peak[0] = peak_image->GetPixel(idx4);
           idx4[3] = 1;
           peak[1] = peak_image->GetPixel(idx4);
           idx4[3] = 2;
           peak[2] = peak_image->GetPixel(idx4);
           if (std::isnan(peak[0]) || std::isnan(peak[1]) || std::isnan(peak[2]) || peak.magnitude()<0.0001f)
             continue;
           peak.normalize();
           
           double f = 1.0 - std::acos(std::fabs(static_cast<double>(dot_product(fdir, peak)))) * 2.0/itk::Math::pi;
           aligned_length += segment.second * f;
         }
         length_sum += segment.second;
       }
     }
   }
 
   if (length_sum<=0.0001)
   {
     MITK_INFO << "Fiber length sum is zero!";
     return std::make_tuple(0,0);
   }
   return std::make_tuple(aligned_length/length_sum, in_mask_length/length_sum);
 }
 
 float mitk::FiberBundle::GetOverlap(ItkUcharImgType* mask)
 {
   vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
 
   MITK_INFO << "Calculating overlap";
   auto spacing = mask->GetSpacing();
   boost::timer::progress_display disp(m_NumFibers);
   double length_sum = 0;
   double in_mask_length = 0;
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = PolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     for (int j=0; j<numPoints-1; j++)
     {
       itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
       itk::Index<3> startIndex;
       itk::ContinuousIndex<float, 3> startIndexCont;
       mask->TransformPhysicalPointToIndex(startVertex, startIndex);
       mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
 
       itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
       itk::Index<3> endIndex;
       itk::ContinuousIndex<float, 3> endIndexCont;
       mask->TransformPhysicalPointToIndex(endVertex, endIndex);
       mask->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 > segment : segments)
       {
         if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
           in_mask_length += segment.second;
         length_sum += segment.second;
       }
     }
   }
 
   if (length_sum<=0.000001)
   {
     MITK_INFO << "Fiber length sum is zero!";
     return 0;
   }
   return static_cast<float>(in_mask_length/length_sum);
 }
 
 mitk::FiberBundle::Pointer mitk::FiberBundle::RemoveFibersOutside(ItkUcharImgType* mask, bool invert)
 {
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   std::vector< float > fib_weights;
 
   MITK_INFO << "Cutting fibers";
   boost::timer::progress_display disp(m_NumFibers);
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
 
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     int newNumPoints = 0;
     if (numPoints>1)
     {
       for (int j=0; j<numPoints; j++)
       {
         itk::Point<float, 3> itkP =mitk::imv::GetItkPoint(points->GetPoint(j));
         itk::Index<3> idx;
         mask->TransformPhysicalPointToIndex(itkP, idx);
 
         bool inside = false;
         if ( mask->GetLargestPossibleRegion().IsInside(idx) && mask->GetPixel(idx)!=0 )
           inside = true;
 
         if (inside && !invert)
         {
           vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
           container->GetPointIds()->InsertNextId(id);
           newNumPoints++;
         }
         else if ( !inside && invert )
         {
           vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
           container->GetPointIds()->InsertNextId(id);
           newNumPoints++;
         }
         else if (newNumPoints>1)
         {
           fib_weights.push_back(this->GetFiberWeight(i));
           vtkNewCells->InsertNextCell(container);
           newNumPoints = 0;
           container = vtkSmartPointer<vtkPolyLine>::New();
         }
         else
         {
           newNumPoints = 0;
           container = vtkSmartPointer<vtkPolyLine>::New();
         }
       }
 
       if (newNumPoints>1)
       {
         fib_weights.push_back(this->GetFiberWeight(i));
         vtkNewCells->InsertNextCell(container);
       }
     }
 
   }
 
   vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
   newFiberWeights->SetName("FIBER_WEIGHTS");
   newFiberWeights->SetNumberOfValues(static_cast<vtkIdType>(fib_weights.size()));
 
   if (vtkNewCells->GetNumberOfCells()<=0)
     return nullptr;
 
   for (unsigned int i=0; i<newFiberWeights->GetNumberOfValues(); i++)
     newFiberWeights->SetValue(i, fib_weights.at(i));
 
 //  vtkSmartPointer<vtkUnsignedCharArray> newFiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
 //  newFiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
 //  newFiberColors->SetNumberOfComponents(4);
 //  newFiberColors->SetName("FIBER_COLORS");
 
 //  unsigned char rgba[4] = {0,0,0,0};
 //  for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
 //  {
 //    rgba[0] = (unsigned char) r;
 //    rgba[1] = (unsigned char) g;
 //    rgba[2] = (unsigned char) b;
 //    rgba[3] = (unsigned char) alpha;
 //    m_FiberColors->InsertTypedTuple(i, rgba);
 //  }
 
   vtkSmartPointer<vtkPolyData> newPolyData = vtkSmartPointer<vtkPolyData>::New();
   newPolyData->SetPoints(vtkNewPoints);
   newPolyData->SetLines(vtkNewCells);
   mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(newPolyData);
   newFib->SetFiberWeights(newFiberWeights);
 //  newFib->Compress(0.1);
   newFib->SetTrackVisHeader(this->GetTrackVisHeader());
   return newFib;
 }
 
 mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset(DataNode* roi, DataStorage* storage)
 {
   if (roi==nullptr || !(dynamic_cast<PlanarFigure*>(roi->GetData()) || dynamic_cast<PlanarFigureComposite*>(roi->GetData())) )
     return nullptr;
 
   std::vector<unsigned int> tmp = ExtractFiberIdSubset(roi, storage);
 
   if (tmp.size()<=0)
     return mitk::FiberBundle::New();
   vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
   vtkSmartPointer<vtkPolyData> pTmp = GeneratePolyDataByIds(tmp, weights);
   mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
   fib->SetFiberWeights(weights);
   fib->SetTrackVisHeader(this->GetTrackVisHeader());
   return fib;
 }
 
 std::vector<unsigned int> mitk::FiberBundle::ExtractFiberIdSubset(DataNode *roi, DataStorage* storage)
 {
   std::vector<unsigned int> result;
   if (roi==nullptr || roi->GetData()==nullptr)
     return result;
 
   mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast<mitk::PlanarFigureComposite*>(roi->GetData());
   if (!pfc.IsNull()) // handle composite
   {
     DataStorage::SetOfObjects::ConstPointer children = storage->GetDerivations(roi);
     if (children->size()==0)
       return result;
 
     switch (pfc->getOperationType())
     {
     case 0: // AND
     {
       MITK_INFO << "AND";
       result = this->ExtractFiberIdSubset(children->ElementAt(0), storage);
       std::vector<unsigned int>::iterator it;
       for (unsigned int i=1; i<children->Size(); ++i)
       {
         std::vector<unsigned int> inRoi = this->ExtractFiberIdSubset(children->ElementAt(i), storage);
 
         std::vector<unsigned int> rest(std::min(result.size(),inRoi.size()));
         it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
         rest.resize( static_cast<unsigned int>(it - rest.begin()) );
         result = rest;
       }
       break;
     }
     case 1: // OR
     {
       MITK_INFO << "OR";
       result = ExtractFiberIdSubset(children->ElementAt(0), storage);
       std::vector<unsigned int>::iterator it;
       for (unsigned int i=1; i<children->Size(); ++i)
       {
         it = result.end();
         std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
         result.insert(it, inRoi.begin(), inRoi.end());
       }
 
       // remove duplicates
       sort(result.begin(), result.end());
       it = unique(result.begin(), result.end());
       result.resize( static_cast<unsigned int>(it - result.begin()) );
       break;
     }
     case 2: // NOT
     {
       MITK_INFO << "NOT";
       for(unsigned int i=0; i<this->GetNumFibers(); i++)
         result.push_back(i);
 
       std::vector<unsigned int>::iterator it;
       for (unsigned int i=0; i<children->Size(); ++i)
       {
         std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
 
         std::vector<unsigned int> rest(result.size()-inRoi.size());
         it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
         rest.resize( static_cast<unsigned int>(it - rest.begin()) );
         result = rest;
       }
       break;
     }
     }
   }
   else if ( dynamic_cast<mitk::PlanarFigure*>(roi->GetData()) )  // actual extraction
   {
     if ( dynamic_cast<mitk::PlanarPolygon*>(roi->GetData()) )
     {
       mitk::PlanarFigure::Pointer planarPoly = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
 
       //create vtkPolygon using controlpoints from planarFigure polygon
       vtkSmartPointer<vtkPolygon> polygonVtk = vtkSmartPointer<vtkPolygon>::New();
       for (unsigned int i=0; i<planarPoly->GetNumberOfControlPoints(); ++i)
       {
         itk::Point<double,3> p = planarPoly->GetWorldControlPoint(i);
         vtkIdType id = polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] );
         polygonVtk->GetPointIds()->InsertNextId(id);
       }
 
       MITK_INFO << "Extracting with polygon";
       boost::timer::progress_display disp(m_NumFibers);
       for (unsigned int i=0; i<m_NumFibers; i++)
       {
         ++disp ;
         vtkCell* cell = m_FiberPolyData->GetCell(i);
         auto numPoints = cell->GetNumberOfPoints();
         vtkPoints* points = cell->GetPoints();
 
         for (int j=0; j<numPoints-1; j++)
         {
           // Inputs
           double p1[3] = {0,0,0};
           points->GetPoint(j, p1);
           double p2[3] = {0,0,0};
           points->GetPoint(j+1, p2);
           double tolerance = 0.001;
 
           // Outputs
           double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
           double x[3] = {0,0,0}; // The coordinate of the intersection
           double pcoords[3] = {0,0,0};
           int subId = 0;
 
           int iD = polygonVtk->IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId);
           if (iD!=0)
           {
             result.push_back(i);
             break;
           }
         }
       }
     }
     else if ( dynamic_cast<mitk::PlanarCircle*>(roi->GetData()) )
     {
       mitk::PlanarFigure::Pointer planarFigure = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
       Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal();
       planeNormal.Normalize();
 
       //calculate circle radius
       mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint
       mitk::Point3D V2w  = planarFigure->GetWorldControlPoint(1); //radiusPoint
 
       double radius = V1w.EuclideanDistanceTo(V2w);
       radius *= radius;
 
       MITK_INFO << "Extracting with circle";
       boost::timer::progress_display disp(m_NumFibers);
       for (unsigned int i=0; i<m_NumFibers; i++)
       {
         ++disp ;
         vtkCell* cell = m_FiberPolyData->GetCell(i);
         auto numPoints = cell->GetNumberOfPoints();
         vtkPoints* points = cell->GetPoints();
 
         for (int j=0; j<numPoints-1; j++)
         {
           // Inputs
           double p1[3] = {0,0,0};
           points->GetPoint(j, p1);
           double p2[3] = {0,0,0};
           points->GetPoint(j+1, p2);
 
           // Outputs
           double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
           double x[3] = {0,0,0}; // The coordinate of the intersection
 
           int iD = vtkPlane::IntersectWithLine(p1,p2,planeNormal.GetDataPointer(),V1w.GetDataPointer(),t,x);
 
           if (iD!=0)
           {
             double dist = (x[0]-V1w[0])*(x[0]-V1w[0])+(x[1]-V1w[1])*(x[1]-V1w[1])+(x[2]-V1w[2])*(x[2]-V1w[2]);
             if( dist <= radius)
             {
               result.push_back(i);
               break;
             }
           }
         }
       }
     }
     return result;
   }
 
   return result;
 }
 
 void mitk::FiberBundle::UpdateFiberGeometry()
 {
   vtkSmartPointer<vtkCleanPolyData> cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
   cleaner->SetInputData(m_FiberPolyData);
   cleaner->PointMergingOff();
   cleaner->Update();
   m_FiberPolyData = cleaner->GetOutput();
 
   m_FiberLengths.clear();
   m_MeanFiberLength = 0;
   m_MedianFiberLength = 0;
   m_LengthStDev = 0;
   m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfCells());
 
   if (m_FiberColors==nullptr || m_FiberColors->GetNumberOfTuples()!=m_FiberPolyData->GetNumberOfPoints())
     this->ColorFibersByOrientation();
 
   if (m_FiberWeights->GetNumberOfValues()!=m_NumFibers)
   {
     m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
     m_FiberWeights->SetName("FIBER_WEIGHTS");
     m_FiberWeights->SetNumberOfValues(m_NumFibers);
     this->SetFiberWeights(1);
   }
 
   if (m_NumFibers<=0) // no fibers present; apply default geometry
   {
     m_MinFiberLength = 0;
     m_MaxFiberLength = 0;
     mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
     geometry->SetImageGeometry(false);
     float b[] = {0, 1, 0, 1, 0, 1};
     geometry->SetFloatBounds(b);
     SetGeometry(geometry);
     return;
   }
   double b[6];
   m_FiberPolyData->GetBounds(b);
 
   // calculate statistics
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto p = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
     float length = 0;
     for (int j=0; j<p-1; j++)
     {
       double p1[3];
       points->GetPoint(j, p1);
       double p2[3];
       points->GetPoint(j+1, p2);
 
       double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
       length += static_cast<float>(dist);
     }
     m_FiberLengths.push_back(length);
     m_MeanFiberLength += length;
     if (i==0)
     {
       m_MinFiberLength = length;
       m_MaxFiberLength = length;
     }
     else
     {
       if (length<m_MinFiberLength)
         m_MinFiberLength = length;
       if (length>m_MaxFiberLength)
         m_MaxFiberLength = length;
     }
   }
   m_MeanFiberLength /= m_NumFibers;
 
   std::vector< float > sortedLengths = m_FiberLengths;
   std::sort(sortedLengths.begin(), sortedLengths.end());
   for (unsigned int i=0; i<m_NumFibers; i++)
     m_LengthStDev += (m_MeanFiberLength-sortedLengths.at(i))*(m_MeanFiberLength-sortedLengths.at(i));
   if (m_NumFibers>1)
     m_LengthStDev /= (m_NumFibers-1);
   else
     m_LengthStDev = 0;
   m_LengthStDev = std::sqrt(m_LengthStDev);
   m_MedianFiberLength = sortedLengths.at(m_NumFibers/2);
 
   mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
   geometry->SetFloatBounds(b);
   this->SetGeometry(geometry);
 
   GetTrackVisHeader();
 
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 float mitk::FiberBundle::GetFiberWeight(unsigned int fiber) const
 {
   return m_FiberWeights->GetValue(fiber);
 }
 
 void mitk::FiberBundle::SetFiberWeights(float newWeight)
 {
   for (int i=0; i<m_FiberWeights->GetNumberOfValues(); i++)
     m_FiberWeights->SetValue(i, newWeight);
 }
 
 void mitk::FiberBundle::SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights)
 {
   if (m_NumFibers!=weights->GetNumberOfValues())
   {
     MITK_INFO << "Weights array not equal to number of fibers! " << weights->GetNumberOfValues() << " vs " << m_NumFibers;
     return;
   }
 
   for (int i=0; i<weights->GetNumberOfValues(); i++)
     m_FiberWeights->SetValue(i, weights->GetValue(i));
 
   m_FiberWeights->SetName("FIBER_WEIGHTS");
 }
 
 void mitk::FiberBundle::SetFiberWeight(unsigned int fiber, float weight)
 {
   m_FiberWeights->SetValue(fiber, weight);
 }
 
 void mitk::FiberBundle::SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors)
 {
   for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
   {
     unsigned char source[4] = {0,0,0,0};
     fiberColors->GetTypedTuple(i, source);
 
     unsigned char target[4] = {0,0,0,0};
     target[0] = source[0];
     target[1] = source[1];
     target[2] = source[2];
     target[3] = source[3];
     m_FiberColors->InsertTypedTuple(i, target);
   }
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 itk::Matrix< double, 3, 3 > mitk::FiberBundle::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz)
 {
   rx = rx*itk::Math::pi/180;
   ry = ry*itk::Math::pi/180;
   rz = rz*itk::Math::pi/180;
 
   itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
   rotX[1][1] = cos(rx);
   rotX[2][2] = rotX[1][1];
   rotX[1][2] = -sin(rx);
   rotX[2][1] = -rotX[1][2];
 
   itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
   rotY[0][0] = cos(ry);
   rotY[2][2] = rotY[0][0];
   rotY[0][2] = sin(ry);
   rotY[2][0] = -rotY[0][2];
 
   itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
   rotZ[0][0] = cos(rz);
   rotZ[1][1] = rotZ[0][0];
   rotZ[0][1] = -sin(rz);
   rotZ[1][0] = -rotZ[0][1];
 
   itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX;
 
   m = rot*m;
 
   return m;
 }
 
 void mitk::FiberBundle::TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform)
 {
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       itk::Point<float, 3> p =mitk::imv::GetItkPoint(points->GetPoint(j));
       p = transform->TransformPoint(p);
       vtkIdType id = vtkNewPoints->InsertNextPoint(p.GetDataPointer());
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz)
 {
   vnl_matrix_fixed< double, 3, 3 > rot = mitk::imv::GetRotationMatrixVnl(rx, ry, rz);
 
   mitk::BaseGeometry::Pointer geom = this->GetGeometry();
   mitk::Point3D center = geom->GetCenter();
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
       vnl_vector_fixed< double, 3 > dir;
       dir[0] = p[0]-center[0];
       dir[1] = p[1]-center[1];
       dir[2] = p[2]-center[2];
       dir = rot*dir;
       dir[0] += center[0]+tx;
       dir[1] += center[1]+ty;
       dir[2] += center[2]+tz;
       vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::RotateAroundAxis(double x, double y, double z)
 {
   x = x*itk::Math::pi/180;
   y = y*itk::Math::pi/180;
   z = z*itk::Math::pi/180;
 
   vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
   rotX[1][1] = cos(x);
   rotX[2][2] = rotX[1][1];
   rotX[1][2] = -sin(x);
   rotX[2][1] = -rotX[1][2];
 
   vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
   rotY[0][0] = cos(y);
   rotY[2][2] = rotY[0][0];
   rotY[0][2] = sin(y);
   rotY[2][0] = -rotY[0][2];
 
   vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
   rotZ[0][0] = cos(z);
   rotZ[1][1] = rotZ[0][0];
   rotZ[0][1] = -sin(z);
   rotZ[1][0] = -rotZ[0][1];
 
   mitk::BaseGeometry::Pointer geom = this->GetGeometry();
   mitk::Point3D center = geom->GetCenter();
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
       vnl_vector_fixed< double, 3 > dir;
       dir[0] = p[0]-center[0];
       dir[1] = p[1]-center[1];
       dir[2] = p[2]-center[2];
       dir = rotZ*rotY*rotX*dir;
       dir[0] += center[0];
       dir[1] += center[1];
       dir[2] += center[2];
       vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   auto colors = GetFiberColors();
   this->SetFiberPolyData(m_FiberPolyData, true);
   SetFiberColors(colors);
 }
 
 void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter)
 {
   MITK_INFO << "Scaling fibers";
   boost::timer::progress_display disp(m_NumFibers);
 
   mitk::BaseGeometry* geom = this->GetGeometry();
   mitk::Point3D c = geom->GetCenter();
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp ;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
       if (subtractCenter)
       {
         p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2];
       }
       p[0] *= x;
       p[1] *= y;
       p[2] *= z;
       if (subtractCenter)
       {
         p[0] += c[0]; p[1] += c[1]; p[2] += c[2];
       }
       vtkIdType id = vtkNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::TranslateFibers(double x, double y, double z)
 {
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
       p[0] += x;
       p[1] += y;
       p[2] += z;
       vtkIdType id = vtkNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::MirrorFibers(unsigned int axis)
 {
   if (axis>2)
     return;
 
   MITK_INFO << "Mirroring fibers";
   boost::timer::progress_display disp(m_NumFibers);
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
       p[axis] = -p[axis];
       vtkIdType id = vtkNewPoints->InsertNextPoint(p);
       container->GetPointIds()->InsertNextId(id);
     }
     vtkNewCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::RemoveDir(vnl_vector_fixed<double,3> dir, double threshold)
 {
   dir.normalize();
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     ++disp ;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     // calculate curvatures
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     bool discard = false;
     for (int j=0; j<numPoints-1; j++)
     {
       double p1[3];
       points->GetPoint(j, p1);
       double p2[3];
       points->GetPoint(j+1, p2);
 
       vnl_vector_fixed< double, 3 > v1;
       v1[0] = p2[0]-p1[0];
       v1[1] = p2[1]-p1[1];
       v1[2] = p2[2]-p1[2];
       if (v1.magnitude()>0.001)
       {
         v1.normalize();
 
         if (fabs(dot_product(v1,dir))>threshold)
         {
           discard = true;
           break;
         }
       }
     }
     if (!discard)
     {
       for (int j=0; j<numPoints; j++)
       {
         double p1[3];
         points->GetPoint(j, p1);
 
         vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
         container->GetPointIds()->InsertNextId(id);
       }
       vtkNewCells->InsertNextCell(container);
     }
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
 
   this->SetFiberPolyData(m_FiberPolyData, true);
 
   //    UpdateColorCoding();
   //    UpdateFiberGeometry();
 }
 
 bool mitk::FiberBundle::ApplyCurvatureThreshold(float minRadius, bool deleteFibers)
 {
   if (minRadius<0)
     return true;
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   MITK_INFO << "Applying curvature threshold";
   boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     ++disp ;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     // calculate curvatures
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     for (int j=0; j<numPoints-2; j++)
     {
       double p1[3];
       points->GetPoint(j, p1);
       double p2[3];
       points->GetPoint(j+1, p2);
       double p3[3];
       points->GetPoint(j+2, p3);
 
       vnl_vector_fixed< float, 3 > v1, v2, v3;
 
       v1[0] = static_cast<float>(p2[0]-p1[0]);
       v1[1] = static_cast<float>(p2[1]-p1[1]);
       v1[2] = static_cast<float>(p2[2]-p1[2]);
 
       v2[0] = static_cast<float>(p3[0]-p2[0]);
       v2[1] = static_cast<float>(p3[1]-p2[1]);
       v2[2] = static_cast<float>(p3[2]-p2[2]);
 
       v3[0] = static_cast<float>(p1[0]-p3[0]);
       v3[1] = static_cast<float>(p1[1]-p3[1]);
       v3[2] = static_cast<float>(p1[2]-p3[2]);
 
       float a = v1.magnitude();
       float b = v2.magnitude();
       float c = v3.magnitude();
       float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
 
       vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
       container->GetPointIds()->InsertNextId(id);
 
       if (deleteFibers && r<minRadius)
         break;
 
       if (r<minRadius)
       {
         j += 2;
         vtkNewCells->InsertNextCell(container);
         container = vtkSmartPointer<vtkPolyLine>::New();
       }
       else if (j==numPoints-3)
       {
         id = vtkNewPoints->InsertNextPoint(p2);
         container->GetPointIds()->InsertNextId(id);
         id = vtkNewPoints->InsertNextPoint(p3);
         container->GetPointIds()->InsertNextId(id);
         vtkNewCells->InsertNextCell(container);
       }
     }
   }
 
   if (vtkNewCells->GetNumberOfCells()<=0)
     return false;
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
   return true;
 }
 
 bool mitk::FiberBundle::RemoveShortFibers(float lengthInMM)
 {
   MITK_INFO << "Removing short fibers";
   if (lengthInMM<=0 || lengthInMM<m_MinFiberLength)
   {
     MITK_INFO << "No fibers shorter than " << lengthInMM << " mm found!";
     return true;
   }
 
   if (lengthInMM>m_MaxFiberLength)    // can't remove all fibers
   {
     MITK_WARN << "Process aborted. No fibers would be left!";
     return false;
   }
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
   float min = m_MaxFiberLength;
 
   boost::timer::progress_display disp(m_NumFibers);
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     if (m_FiberLengths.at(i)>=lengthInMM)
     {
       vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
       for (int j=0; j<numPoints; j++)
       {
         double* p = points->GetPoint(j);
         vtkIdType id = vtkNewPoints->InsertNextPoint(p);
         container->GetPointIds()->InsertNextId(id);
       }
       vtkNewCells->InsertNextCell(container);
       if (m_FiberLengths.at(i)<min)
         min = m_FiberLengths.at(i);
     }
   }
 
   if (vtkNewCells->GetNumberOfCells()<=0)
     return false;
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
   return true;
 }
 
 bool mitk::FiberBundle::RemoveLongFibers(float lengthInMM)
 {
   if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength)
     return true;
 
   if (lengthInMM<m_MinFiberLength)    // can't remove all fibers
     return false;
 
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   MITK_INFO << "Removing long fibers";
   boost::timer::progress_display disp(m_NumFibers);
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     ++disp;
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     if (m_FiberLengths.at(i)<=lengthInMM)
     {
       vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
       for (int j=0; j<numPoints; j++)
       {
         double* p = points->GetPoint(j);
         vtkIdType id = vtkNewPoints->InsertNextPoint(p);
         container->GetPointIds()->InsertNextId(id);
       }
       vtkNewCells->InsertNextCell(container);
     }
   }
 
   if (vtkNewCells->GetNumberOfCells()<=0)
     return false;
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkNewPoints);
   m_FiberPolyData->SetLines(vtkNewCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
   return true;
 }
 
 void mitk::FiberBundle::ResampleSpline(float pointDistance, double tension, double continuity, double bias )
 {
   if (pointDistance<=0)
     return;
 
   vtkSmartPointer<vtkPoints> vtkSmoothPoints = vtkSmartPointer<vtkPoints>::New(); //in smoothpoints the interpolated points representing a fiber are stored.
 
   //in vtkcells all polylines are stored, actually all id's of them are stored
   vtkSmartPointer<vtkCellArray> vtkSmoothCells = vtkSmartPointer<vtkCellArray>::New(); //cellcontainer for smoothed lines
 
   MITK_INFO << "Smoothing fibers";
   vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
   newFiberWeights->SetName("FIBER_WEIGHTS");
   newFiberWeights->SetNumberOfValues(m_NumFibers);
 
   std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
   resampled_streamlines.resize(m_NumFibers);
 
   boost::timer::progress_display disp(m_NumFibers);
 #pragma omp parallel for
   for (int i=0; i<static_cast<int>(m_NumFibers); i++)
   {
     vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
     float length = 0;
 #pragma omp critical
     {
       length = m_FiberLengths.at(static_cast<unsigned int>(i));
       ++disp;
       vtkCell* cell = m_FiberPolyData->GetCell(i);
       auto numPoints = cell->GetNumberOfPoints();
       vtkPoints* points = cell->GetPoints();
       for (int j=0; j<numPoints; j++)
         newPoints->InsertNextPoint(points->GetPoint(j));
     }
 
     int sampling = static_cast<int>(std::ceil(length/pointDistance));
 
     vtkSmartPointer<vtkKochanekSpline> xSpline = vtkSmartPointer<vtkKochanekSpline>::New();
     vtkSmartPointer<vtkKochanekSpline> ySpline = vtkSmartPointer<vtkKochanekSpline>::New();
     vtkSmartPointer<vtkKochanekSpline> zSpline = vtkSmartPointer<vtkKochanekSpline>::New();
     xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity);
     ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity);
     zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity);
 
     vtkSmartPointer<vtkParametricSpline> spline = vtkSmartPointer<vtkParametricSpline>::New();
     spline->SetXSpline(xSpline);
     spline->SetYSpline(ySpline);
     spline->SetZSpline(zSpline);
     spline->SetPoints(newPoints);
 
     vtkSmartPointer<vtkParametricFunctionSource> functionSource = vtkSmartPointer<vtkParametricFunctionSource>::New();
     functionSource->SetParametricFunction(spline);
     functionSource->SetUResolution(sampling);
     functionSource->SetVResolution(sampling);
     functionSource->SetWResolution(sampling);
     functionSource->Update();
 
     vtkPolyData* outputFunction = functionSource->GetOutput();
     vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber
 
     vtkSmartPointer<vtkPolyLine> smoothLine = vtkSmartPointer<vtkPolyLine>::New();
 
 #pragma omp critical
     {
       for (int j=0; j<tmpSmoothPnts->GetNumberOfPoints(); j++)
       {
         vtkIdType id = vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j));
         smoothLine->GetPointIds()->InsertNextId(id);
       }
 
       resampled_streamlines[static_cast<unsigned long>(i)] = smoothLine;
     }
   }
 
   for (auto container : resampled_streamlines)
   {
     vtkSmoothCells->InsertNextCell(container);
   }
 
   m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
   m_FiberPolyData->SetPoints(vtkSmoothPoints);
   m_FiberPolyData->SetLines(vtkSmoothCells);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::ResampleSpline(float pointDistance)
 {
   ResampleSpline(pointDistance, 0, 0, 0 );
 }
 
 unsigned int mitk::FiberBundle::GetNumberOfPoints() const
 {
   unsigned int points = 0;
   for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     points += cell->GetNumberOfPoints();
   }
   return points;
 }
 
 void mitk::FiberBundle::Compress(float error)
 {
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   MITK_INFO << "Compressing fibers with max. error " << error << "mm";
   unsigned int numRemovedPoints = 0;
   boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
   vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
   newFiberWeights->SetName("FIBER_WEIGHTS");
   newFiberWeights->SetNumberOfValues(m_NumFibers);
 
 #pragma omp parallel for
   for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
   {
 
     std::vector< vnl_vector_fixed< double, 3 > > vertices;
     float weight = 1;
 
 #pragma omp critical
     {
       ++disp;
       weight = m_FiberWeights->GetValue(i);
       vtkCell* cell = m_FiberPolyData->GetCell(i);
       auto numPoints = cell->GetNumberOfPoints();
       vtkPoints* points = cell->GetPoints();
 
       for (int j=0; j<numPoints; j++)
       {
         double cand[3];
         points->GetPoint(j, cand);
         vnl_vector_fixed< double, 3 > candV;
         candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
         vertices.push_back(candV);
       }
     }
 
     // calculate curvatures
     auto numPoints = vertices.size();
     std::vector< int > removedPoints; removedPoints.resize(numPoints, 0);
     removedPoints[0]=-1; removedPoints[numPoints-1]=-1;
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     unsigned int remCounter = 0;
 
     bool pointFound = true;
     while (pointFound)
     {
       pointFound = false;
       double minError = static_cast<double>(error);
       unsigned int removeIndex = 0;
 
       for (unsigned int j=0; j<vertices.size(); j++)
       {
         if (removedPoints[j]==0)
         {
           vnl_vector_fixed< double, 3 > candV = vertices.at(j);
 
           int validP = -1;
           vnl_vector_fixed< double, 3 > pred;
           for (int k=static_cast<int>(j)-1; k>=0; k--)
             if (removedPoints[static_cast<unsigned int>(k)]<=0)
             {
               pred = vertices.at(static_cast<unsigned int>(k));
               validP = k;
               break;
             }
           int validS = -1;
           vnl_vector_fixed< double, 3 > succ;
           for (unsigned int k=j+1; k<numPoints; k++)
             if (removedPoints[k]<=0)
             {
               succ = vertices.at(k);
               validS = static_cast<int>(k);
               break;
             }
 
           if (validP>=0 && validS>=0)
           {
             double a = (candV-pred).magnitude();
             double b = (candV-succ).magnitude();
             double c = (pred-succ).magnitude();
             double s=0.5*(a+b+c);
             double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c)));
 
             if (hc<minError)
             {
               removeIndex = j;
               minError = hc;
               pointFound = true;
             }
           }
         }
       }
 
       if (pointFound)
       {
         removedPoints[removeIndex] = 1;
         remCounter++;
       }
     }
 
     for (unsigned int j=0; j<numPoints; j++)
     {
       if (removedPoints[j]<=0)
       {
 #pragma omp critical
         {
           vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
           container->GetPointIds()->InsertNextId(id);
         }
       }
     }
 
 #pragma omp critical
     {
       newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
       numRemovedPoints += remCounter;
       vtkNewCells->InsertNextCell(container);
     }
   }
 
   if (vtkNewCells->GetNumberOfCells()>0)
   {
     MITK_INFO << "Removed points: " << numRemovedPoints;
     SetFiberWeights(newFiberWeights);
     m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     m_FiberPolyData->SetPoints(vtkNewPoints);
     m_FiberPolyData->SetLines(vtkNewCells);
     this->SetFiberPolyData(m_FiberPolyData, true);
   }
 }
 
 void mitk::FiberBundle::ResampleToNumPoints(unsigned int targetPoints)
 {
   if (targetPoints<2)
     mitkThrow() << "Minimum two points required for resampling!";
 
   MITK_INFO << "Resampling fibers (number of points " << targetPoints << ")";
 
   bool unequal_fibs = true;
   while (unequal_fibs)
   {
     vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
     vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
     vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
     newFiberWeights->SetName("FIBER_WEIGHTS");
     newFiberWeights->SetNumberOfValues(m_NumFibers);
 
     unequal_fibs = false;
     for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
     {
 
       std::vector< vnl_vector_fixed< double, 3 > > vertices;
       float weight = 1;
       double seg_len = 0;
 
       {
         weight = m_FiberWeights->GetValue(i);
         vtkCell* cell = m_FiberPolyData->GetCell(i);
         auto numPoints = cell->GetNumberOfPoints();
         if (numPoints!=targetPoints)
           seg_len = static_cast<double>(this->GetFiberLength(i)/(targetPoints-1));
         vtkPoints* points = cell->GetPoints();
 
         for (int j=0; j<numPoints; j++)
         {
           double cand[3];
           points->GetPoint(j, cand);
           vnl_vector_fixed< double, 3 > candV;
           candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
           vertices.push_back(candV);
         }
       }
 
       vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
       vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
 
       {
         vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
         container->GetPointIds()->InsertNextId(id);
       }
       for (unsigned int j=1; j<vertices.size(); j++)
       {
         vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
         double new_dist = vec.magnitude();
 
         if (new_dist >= seg_len && seg_len>0)
         {
           vnl_vector_fixed< double, 3 > newV = lastV;
           if ( new_dist-seg_len <= mitk::eps )
           {
             vec.normalize();
             newV += vec * seg_len;
           }
           else
           {
             // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
             vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
             vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
 
             double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2];
             double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
             double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - seg_len*seg_len;
 
             double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a);
             double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a);
 
             if (v1>0)
               newV = p + d * v1;
             else if (v2>0)
               newV = p + d * v2;
             else
               MITK_INFO << "ERROR1 - linear resampling";
 
             j--;
           }
 
 //#pragma omp critical
           {
             vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
             container->GetPointIds()->InsertNextId(id);
           }
           lastV = newV;
         }
         else if ( (j==vertices.size()-1 && new_dist>0.0001) || seg_len<=0.0000001)
         {
 //#pragma omp critical
           {
             vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
             container->GetPointIds()->InsertNextId(id);
           }
         }
       }
 
 //#pragma omp critical
       {
         newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
         vtkNewCells->InsertNextCell(container);
         if (container->GetNumberOfPoints()!=targetPoints)
           unequal_fibs = true;
       }
     }
 
     if (vtkNewCells->GetNumberOfCells()>0)
     {
       SetFiberWeights(newFiberWeights);
       m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
       m_FiberPolyData->SetPoints(vtkNewPoints);
       m_FiberPolyData->SetLines(vtkNewCells);
       this->SetFiberPolyData(m_FiberPolyData, true);
     }
   }
 }
 
 void mitk::FiberBundle::ResampleLinear(double pointDistance)
 {
   vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
 
   MITK_INFO << "Resampling fibers (linear)";
   boost::timer::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
   vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
   newFiberWeights->SetName("FIBER_WEIGHTS");
   newFiberWeights->SetNumberOfValues(m_NumFibers);
 
   std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
   resampled_streamlines.resize(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
 
 #pragma omp parallel for
   for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
   {
 
     std::vector< vnl_vector_fixed< double, 3 > > vertices;
 
 #pragma omp critical
     {
       ++disp;
       vtkCell* cell = m_FiberPolyData->GetCell(i);
       auto numPoints = cell->GetNumberOfPoints();
       vtkPoints* points = cell->GetPoints();
 
       for (int j=0; j<numPoints; j++)
       {
         double cand[3];
         points->GetPoint(j, cand);
         vnl_vector_fixed< double, 3 > candV;
         candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
         vertices.push_back(candV);
       }
     }
 
     vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
     vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
 
 #pragma omp critical
     {
       vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
       container->GetPointIds()->InsertNextId(id);
     }
     for (unsigned int j=1; j<vertices.size(); j++)
     {
       vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
       double new_dist = vec.magnitude();
 
       if (new_dist >= pointDistance)
       {
         vnl_vector_fixed< double, 3 > newV = lastV;
         if ( new_dist-pointDistance <= mitk::eps )
         {
           vec.normalize();
           newV += vec * pointDistance;
         }
         else
         {
           // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
           vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
           vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
 
           double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2];
           double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
           double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - pointDistance*pointDistance;
 
           double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a);
           double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a);
 
           if (v1>0)
             newV = p + d * v1;
           else if (v2>0)
             newV = p + d * v2;
           else
             MITK_INFO << "ERROR1 - linear resampling";
 
           j--;
         }
 
 #pragma omp critical
         {
           vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
           container->GetPointIds()->InsertNextId(id);
         }
         lastV = newV;
       }
       else if (j==vertices.size()-1 && new_dist>0.0001)
       {
 #pragma omp critical
         {
           vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
           container->GetPointIds()->InsertNextId(id);
         }
       }
     }
 
 #pragma omp critical
     {
       resampled_streamlines[static_cast<unsigned int>(i)] = container;
     }
   }
 
   for (auto container : resampled_streamlines)
   {
     vtkNewCells->InsertNextCell(container);
   }
 
   if (vtkNewCells->GetNumberOfCells()>0)
   {
     m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     m_FiberPolyData->SetPoints(vtkNewPoints);
     m_FiberPolyData->SetLines(vtkNewCells);
     this->SetFiberPolyData(m_FiberPolyData, true);
   }
 }
 
 // reapply selected colorcoding in case PolyData structure has changed
 bool mitk::FiberBundle::Equals(mitk::FiberBundle* fib, double eps)
 {
   if (fib==nullptr)
   {
     MITK_INFO << "Reference bundle is nullptr!";
     return false;
   }
 
   if (m_NumFibers!=fib->GetNumFibers())
   {
     MITK_INFO << "Unequal number of fibers!";
     MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers();
     return false;
   }
 
   for (unsigned int i=0; i<m_NumFibers; i++)
   {
     vtkCell* cell = m_FiberPolyData->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i);
     auto numPoints2 = cell2->GetNumberOfPoints();
     vtkPoints* points2 = cell2->GetPoints();
 
     if (numPoints2!=numPoints)
     {
       MITK_INFO << "Unequal number of points in fiber " << i << "!";
       MITK_INFO << numPoints2 << " vs. " << numPoints;
       return false;
     }
 
     for (int j=0; j<numPoints; j++)
     {
       double* p1 = points->GetPoint(j);
       double* p2 = points2->GetPoint(j);
       if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps)
       {
         MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!";
         MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2];
         MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2];
         return false;
       }
     }
   }
 
   return true;
 }
 
 void mitk::FiberBundle::PrintSelf(std::ostream &os, itk::Indent indent) const
 {
   os << indent << "Number of fibers: " << this->GetNumFibers() << std::endl;
   os << indent << "Min. fiber length: " << this->GetMinFiberLength() << std::endl;
   os << indent << "Max. fiber length: " << this->GetMaxFiberLength() << std::endl;
   os << indent << "Mean fiber length: " << this->GetMeanFiberLength() << std::endl;
   os << indent << "Median fiber length: " << this->GetMedianFiberLength() << std::endl;
   os << indent << "STDEV fiber length: " << this->GetLengthStDev() << std::endl;
   os << indent << "Number of points: " << this->GetNumberOfPoints() << std::endl;
 
   os << indent << "Extent x: " << this->GetGeometry()->GetExtentInMM(0) << "mm" << std::endl;
   os << indent << "Extent y: " << this->GetGeometry()->GetExtentInMM(1) << "mm" << std::endl;
   os << indent << "Extent z: " << this->GetGeometry()->GetExtentInMM(2) << "mm" << std::endl;
   os << indent << "Diagonal: " << this->GetGeometry()->GetDiagonalLength()  << "mm" << std::endl;
 
   os << "\nReference geometry:" << std::endl;
   os << indent << "Size: [" << std::defaultfloat << m_TrackVisHeader.dim[0] << " " << m_TrackVisHeader.dim[1] << " " << m_TrackVisHeader.dim[2] << "]" << std::endl;
   os << indent << "Voxel size: [" << m_TrackVisHeader.voxel_size[0] << " " << m_TrackVisHeader.voxel_size[1] << " " << m_TrackVisHeader.voxel_size[2] << "]" << std::endl;
   os << indent << "Origin: [" << m_TrackVisHeader.origin[0] << " " << m_TrackVisHeader.origin[1] << " " << m_TrackVisHeader.origin[2] << "]" << std::endl;
   os << indent << "Matrix: " << std::scientific << std::endl;
   os << indent << "[[" << m_TrackVisHeader.vox_to_ras[0][0] << ", " << m_TrackVisHeader.vox_to_ras[0][1] << ", " << m_TrackVisHeader.vox_to_ras[0][2] << ", " << m_TrackVisHeader.vox_to_ras[0][3] << "]" << std::endl;
   os << indent << " [" << m_TrackVisHeader.vox_to_ras[1][0] << ", " << m_TrackVisHeader.vox_to_ras[1][1] << ", " << m_TrackVisHeader.vox_to_ras[1][2] << ", " << m_TrackVisHeader.vox_to_ras[1][3] << "]" << std::endl;
   os << indent << " [" << m_TrackVisHeader.vox_to_ras[2][0] << ", " << m_TrackVisHeader.vox_to_ras[2][1] << ", " << m_TrackVisHeader.vox_to_ras[2][2] << ", " << m_TrackVisHeader.vox_to_ras[2][3] << "]" << std::endl;
   os << indent << " [" << m_TrackVisHeader.vox_to_ras[3][0] << ", " << m_TrackVisHeader.vox_to_ras[3][1] << ", " << m_TrackVisHeader.vox_to_ras[3][2] << ", " << m_TrackVisHeader.vox_to_ras[3][3] << "]]" << std::defaultfloat << std::endl;
 
   if (m_FiberWeights!=nullptr)
   {
     std::vector< float > weights;
     for (int i=0; i<m_FiberWeights->GetSize(); i++)
       weights.push_back(m_FiberWeights->GetValue(i));
 
     std::sort(weights.begin(), weights.end());
 
     os << "\nFiber weight statistics" << std::endl;
     os << indent << "Min: " << weights.front() << std::endl;
     os << indent << "1% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.01)) << std::endl;
     os << indent << "5% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.05)) << std::endl;
     os << indent << "25% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.25)) << std::endl;
     os << indent << "Median: " << weights.at(static_cast<unsigned long>(weights.size()*0.5)) << std::endl;
     os << indent << "75% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.75)) << std::endl;
     os << indent << "95% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.95)) << std::endl;
     os << indent << "99% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.99)) << std::endl;
     os << indent << "Max: " << weights.back() << std::endl;
   }
   else
     os << indent << "\n\nNo fiber weight array found." << std::endl;
 
   Superclass::PrintSelf(os, 0);
 }
 
 mitk::FiberBundle::TrackVis_header mitk::FiberBundle::GetTrackVisHeader()
 {
   if (m_TrackVisHeader.hdr_size==0)
   {
     mitk::Geometry3D::Pointer geom = dynamic_cast<mitk::Geometry3D*>(this->GetGeometry());
     SetTrackVisHeader(geom);
   }
   return m_TrackVisHeader;
 }
 
 void mitk::FiberBundle::SetTrackVisHeader(const mitk::FiberBundle::TrackVis_header &TrackVisHeader)
 {
   m_TrackVisHeader = TrackVisHeader;
 }
 
 void mitk::FiberBundle::SetTrackVisHeader(mitk::BaseGeometry* geometry)
 {
   vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
   matrix->Identity();
 
   if (geometry==nullptr)
     return;
 
   for(int i=0; i<3 ;i++)
   {
     m_TrackVisHeader.dim[i]            = geometry->GetExtent(i);
     m_TrackVisHeader.voxel_size[i]     = geometry->GetSpacing()[i];
     m_TrackVisHeader.origin[i]         = geometry->GetOrigin()[i];
     matrix = geometry->GetVtkMatrix();
   }
 
   for (int i=0; i<4; ++i)
     for (int j=0; j<4; ++j)
       m_TrackVisHeader.vox_to_ras[i][j] = matrix->GetElement(i, j);
 
   m_TrackVisHeader.n_scalars = 0;
   m_TrackVisHeader.n_properties = 0;
   sprintf(m_TrackVisHeader.voxel_order,"RAS");
   m_TrackVisHeader.image_orientation_patient[0] = 1.0;
   m_TrackVisHeader.image_orientation_patient[1] = 0.0;
   m_TrackVisHeader.image_orientation_patient[2] = 0.0;
   m_TrackVisHeader.image_orientation_patient[3] = 0.0;
   m_TrackVisHeader.image_orientation_patient[4] = 1.0;
   m_TrackVisHeader.image_orientation_patient[5] = 0.0;
   m_TrackVisHeader.pad1[0] = 0;
   m_TrackVisHeader.pad1[1] = 0;
   m_TrackVisHeader.pad2[0] = 0;
   m_TrackVisHeader.pad2[1] = 0;
   m_TrackVisHeader.invert_x = 0;
   m_TrackVisHeader.invert_y = 0;
   m_TrackVisHeader.invert_z = 0;
   m_TrackVisHeader.swap_xy = 0;
   m_TrackVisHeader.swap_yz = 0;
   m_TrackVisHeader.swap_zx = 0;
   m_TrackVisHeader.n_count = 0;
   m_TrackVisHeader.version = 2;
   m_TrackVisHeader.hdr_size = 1000;
   std::string id = "TRACK";
   strcpy(m_TrackVisHeader.id_string, id.c_str());
 }
 
 /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
 void mitk::FiberBundle::UpdateOutputInformation()
 {
 
 }
 void mitk::FiberBundle::SetRequestedRegionToLargestPossibleRegion()
 {
 
 }
 bool mitk::FiberBundle::RequestedRegionIsOutsideOfTheBufferedRegion()
 {
   return false;
 }
 bool mitk::FiberBundle::VerifyRequestedRegion()
 {
   return true;
 }
 void mitk::FiberBundle::SetRequestedRegion(const itk::DataObject* )
 {
 
 }
diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
index 1b22f33..dfa927c 100644
--- a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
+++ b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
@@ -1,100 +1,100 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center.
 
 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 "mitkFiberBundleTrackVisReader.h"
 #include <itkMetaDataObject.h>
 #include <vtkPolyData.h>
 #include <vtkDataReader.h>
 #include <vtkPolyDataReader.h>
 #include <vtkMatrix4x4.h>
 #include <vtkPolyLine.h>
 #include <vtkCellArray.h>
 #include <vtkDataArray.h>
 #include <vtkFloatArray.h>
 #include <vtkCellData.h>
 #include <vtkPointData.h>
 #include <itksys/SystemTools.hxx>
 #include <vtkCleanPolyData.h>
 #include <mitkTrackvis.h>
 #include <mitkCustomMimeType.h>
 #include "mitkDiffusionIOMimeTypes.h"
 
 
 mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader()
   : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader" )
 {
   Options defaultOptions;
   defaultOptions["Apply index to world transform stored in the TRK header"] = true;
   defaultOptions["Print header"] = true;
-  defaultOptions["Flip x"] = false;
+  defaultOptions["Flip x"] = true;
   defaultOptions["Flip y"] = false;
   defaultOptions["Flip z"] = false;
   this->SetDefaultOptions(defaultOptions);
 
   m_ServiceReg = this->RegisterService();
 }
 
 mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader(const FiberBundleTrackVisReader &other)
   :mitk::AbstractFileReader(other)
 {
 }
 
 mitk::FiberBundleTrackVisReader * mitk::FiberBundleTrackVisReader::Clone() const
 {
   return new FiberBundleTrackVisReader(*this);
 }
 
 std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTrackVisReader::DoRead()
 {
 
   std::vector<itk::SmartPointer<mitk::BaseData> > result;
   try
   {
     const std::string& locale = "C";
     const std::string& currLocale = setlocale( LC_ALL, nullptr );
     setlocale(LC_ALL, locale.c_str());
 
     std::string filename = this->GetInputLocation();
     MITK_INFO << "Loading tractogram (TrackVis format): " << itksys::SystemTools::GetFilenameName(filename);
 
     std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
     ext = itksys::SystemTools::LowerCase(ext);
 
     if (ext==".trk")
     {
       Options options = this->GetOptions();
       bool apply_matrix = us::any_cast<bool>(options["Apply index to world transform stored in the TRK header"]);
       bool flip_x = us::any_cast<bool>(options["Flip x"]);
       bool flip_y = us::any_cast<bool>(options["Flip y"]);
       bool flip_z = us::any_cast<bool>(options["Flip z"]);
       bool print_header = us::any_cast<bool>(options["Print header"]);
       FiberBundle::Pointer mitk_fib = FiberBundle::New();
       TrackVisFiberReader reader;
       reader.open(this->GetInputLocation().c_str());
       reader.read(mitk_fib.GetPointer(), apply_matrix, flip_x, flip_y, flip_z, print_header);
       result.push_back(mitk_fib.GetPointer());
       return result;
     }
 
     setlocale(LC_ALL, currLocale.c_str());
     MITK_INFO << "Fiber bundle read";
   }
   catch(...)
   {
     throw;
   }
   return result;
 }