diff --git a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
index 19e6967..2d8ad41 100644
--- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
+++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp
@@ -1,2820 +1,2820 @@
 /*===================================================================
 
 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 "mitkImagePixelReadAccessor.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/progress.hpp>
 #include <vtkTransformPolyDataFilter.h>
 #include <mitkTransferFunction.h>
 #include <vtkLookupTable.h>
 #include <mitkLookupTable.h>
 #include <vtkCardinalSpline.h>
 #include <vtkAppendPolyData.h>
 
 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_shuffle(ids.begin(), ids.end());
 
   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::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)
+void mitk::FiberBundle::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap)
 {
-  mitkPixelTypeMultiplex4( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity, weight_fibers, type );
+  mitkPixelTypeMultiplex5( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity, weight_fibers, type, max_cap );
   m_UpdateTime3D.Modified();
   m_UpdateTime2D.Modified();
 }
 
 template <typename TPixel>
-void mitk::FiberBundle::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type)
+void mitk::FiberBundle::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap)
 {
   m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
   m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
   m_FiberColors->SetNumberOfComponents(4);
   m_FiberColors->SetName("FIBER_COLORS");
 
   mitk::ImagePixelReadAccessor<TPixel,3> readimage(image, image->GetVolumeData(0));
 
   unsigned char rgba[4] = {0,0,0,0};
   vtkPoints* pointSet = m_FiberPolyData->GetPoints();
 
   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);
 
       Point3D px;
       px[0] = p[0];
       px[1] = p[1];
       px[2] = p[2];
       auto pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
 
       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);
+    mitkLookup->GetVtkLookupTable()->SetTableRange(min, max*max_cap);
 
   for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
   {
     Point3D px;
     px[0] = pointSet->GetPoint(i)[0];
     px[1] = pointSet->GetPoint(i)[1];
     px[2] = pointSet->GetPoint(i)[2];
     auto pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
 
     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::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::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::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::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::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::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);
   this->SetFiberPolyData(m_FiberPolyData, true);
 }
 
 void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter)
 {
   MITK_INFO << "Scaling fibers";
   boost::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::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::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::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::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::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::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::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::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,"LPS");
   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/DiffusionCore/IODataStructures/mitkFiberBundle.h b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
index 23667ae..6766248 100644
--- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
+++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h
@@ -1,247 +1,247 @@
 /*===================================================================
 
 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.
 
 ===================================================================*/
 
 
 #ifndef _MITK_FiberBundle_H
 #define _MITK_FiberBundle_H
 
 //includes for MITK datastructure
 #include <mitkBaseData.h>
 #include <MitkDiffusionCoreExports.h>
 #include <mitkImage.h>
 #include <mitkDataStorage.h>
 #include <mitkPlanarFigure.h>
 #include <mitkPixelTypeTraits.h>
 #include <mitkPlanarFigureComposite.h>
 #include <mitkPeakImage.h>
 
 //includes storing fiberdata
 #include <vtkSmartPointer.h>
 #include <vtkPolyData.h>
 #include <vtkPoints.h>
 #include <vtkDataSet.h>
 #include <vtkTransform.h>
 #include <vtkFloatArray.h>
 #include <itkScalableAffineTransform.h>
 #include <mitkDiffusionFunctionCollection.h>
 #include <mitkLookupTable.h>
 
 namespace mitk {
 
 /**
    * \brief Base Class for Fiber Bundles;   */
 class MITKDIFFUSIONCORE_EXPORT FiberBundle : public BaseData
 {
 public:
 
     typedef itk::Image<unsigned char, 3> ItkUcharImgType;
 
     // fiber colorcodings
     static const char* FIBER_ID_ARRAY;
 
     void UpdateOutputInformation() override;
     void SetRequestedRegionToLargestPossibleRegion() override;
     bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
     bool VerifyRequestedRegion() override;
     void SetRequestedRegion(const itk::DataObject*) override;
 
     mitkClassMacro( FiberBundle, BaseData )
     itkFactorylessNewMacro(Self)
     itkCloneMacro(Self)
     mitkNewMacro1Param(Self, vtkSmartPointer<vtkPolyData>) // custom constructor
 
     // colorcoding related methods
     void ColorSinglePoint(int f_idx, int p_idx, double rgb[3]);
     void ColorFibersByFiberWeights(bool opacity, LookupTable::LookupTableType type);
     void ColorFibersByCurvature(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
     void ColorFibersByLength(bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
-    void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
+    void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap);
     template <typename TPixel>
-    void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type);
+    void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap);
     void ColorFibersByOrientation();
     void SetFiberOpacity(vtkDoubleArray *FAValArray);
     void ResetFiberOpacity();
     void SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors);
     void SetFiberColors(float r, float g, float b, float alpha=255);
     vtkSmartPointer<vtkUnsignedCharArray> GetFiberColors() const { return m_FiberColors; }
 
     // fiber compression
     void Compress(float error = 0.0);
 
     // fiber resampling
     void ResampleSpline(float pointDistance=1);
     void ResampleSpline(float pointDistance, double tension, double continuity, double bias );
     void ResampleLinear(double pointDistance=1);
     void ResampleToNumPoints(unsigned int targetPoints);
 
     mitk::FiberBundle::Pointer FilterByWeights(float weight_thr, bool invert=false);
     bool RemoveShortFibers(float lengthInMM);
     bool RemoveLongFibers(float lengthInMM);
     bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers);
     void MirrorFibers(unsigned int axis);
     void RotateAroundAxis(double x, double y, double z);
     void TranslateFibers(double x, double y, double z);
     void ScaleFibers(double x, double y, double z, bool subtractCenter=true);
     void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz);
     void TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform);
     void RemoveDir(vnl_vector_fixed<double,3> dir, double threshold);
 
     template< class TType=float >
     void TransformPoint(itk::Point<TType, 3>& point, itk::Matrix< TType, 3, 3>& rot, TType& tx, TType& ty, TType& tz)
     {
       mitk::Point3D center = this->GetGeometry()->GetCenter();
 
       point[0] -= center[0];
       point[1] -= center[1];
       point[2] -= center[2];
       point = rot*point;
       point[0] += center[0]+tx;
       point[1] += center[1]+ty;
       point[2] += center[2]+tz;
     }
 
     template< class TType=float >
     void TransformPoint(itk::Point<TType, 3>& point, TType rx, TType ry, TType rz, TType tx, TType ty, TType tz)
     {
       auto rot = mitk::imv::GetRotationMatrixItk<TType>(rx, ry, rz);
       mitk::Point3D center = this->GetGeometry()->GetCenter();
 
       point[0] -= center[0];
       point[1] -= center[1];
       point[2] -= center[2];
       point = rot*point;
       point[0] += center[0]+tx;
       point[1] += center[1]+ty;
       point[2] += center[2]+tz;
     }
 
     itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz);
 
     // add/subtract fibers
     FiberBundle::Pointer AddBundle(FiberBundle* fib);
     mitk::FiberBundle::Pointer AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs);
     FiberBundle::Pointer SubtractBundle(FiberBundle* fib);
 
     // fiber subset extraction
     FiberBundle::Pointer           ExtractFiberSubset(DataNode *roi, DataStorage* storage);
     std::vector<unsigned int>      ExtractFiberIdSubset(DataNode* roi, DataStorage* storage);
     FiberBundle::Pointer           RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false);
     float                          GetOverlap(ItkUcharImgType* mask);
     std::tuple<float, float>       GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image);
     float                          GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label);
     mitk::FiberBundle::Pointer     SubsampleFibers(float factor, bool random_seed);
 
     // get/set data
     float GetFiberLength(unsigned int index) const { return m_FiberLengths.at(index); }
     vtkSmartPointer<vtkFloatArray> GetFiberWeights() const { return m_FiberWeights; }
     float GetFiberWeight(unsigned int fiber) const;
     void SetFiberWeights(float newWeight);
     void SetFiberWeight(unsigned int fiber, float weight);
     void SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights);
     void SetFiberPolyData(vtkSmartPointer<vtkPolyData>, bool updateGeometry = true);
     vtkSmartPointer<vtkPolyData> GetFiberPolyData() const;
     itkGetConstMacro( NumFibers, unsigned int)
     //itkGetMacro( FiberSampling, int)
     itkGetConstMacro( MinFiberLength, float )
     itkGetConstMacro( MaxFiberLength, float )
     itkGetConstMacro( MeanFiberLength, float )
     itkGetConstMacro( MedianFiberLength, float )
     itkGetConstMacro( LengthStDev, float )
     itkGetConstMacro( UpdateTime2D, itk::TimeStamp )
     itkGetConstMacro( UpdateTime3D, itk::TimeStamp )
     void RequestUpdate2D(){ m_UpdateTime2D.Modified(); }
     void RequestUpdate3D(){ m_UpdateTime3D.Modified(); }
     void RequestUpdate(){ m_UpdateTime2D.Modified(); m_UpdateTime3D.Modified(); }
 
     unsigned int GetNumberOfPoints() const;
 
     // copy fiber bundle
     mitk::FiberBundle::Pointer GetDeepCopy();
 
     // compare fiber bundles
     bool Equals(FiberBundle* fib, double eps=0.01);
 
     vtkSmartPointer<vtkPolyData>    GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights);
 
     // Structure to hold metadata of a TrackVis file
     struct TrackVis_header
     {
         char                id_string[6];
         short int           dim[3];
         float               voxel_size[3];
         float               origin[3];
         short int           n_scalars;
         char                scalar_name[10][20];
         short int           n_properties;
         char                property_name[10][20];
         float               vox_to_ras[4][4];
         char                reserved[444];
         char                voxel_order[4];
         char                pad2[4];
         float               image_orientation_patient[6];
         char                pad1[2];
         unsigned char       invert_x;
         unsigned char       invert_y;
         unsigned char       invert_z;
         unsigned char       swap_xy;
         unsigned char       swap_yz;
         unsigned char       swap_zx;
         int                 n_count;
         int                 version;
         int                 hdr_size;
     };
 
     TrackVis_header GetTrackVisHeader();
     void SetTrackVisHeader(const TrackVis_header &TrackVisHeader);
     void SetTrackVisHeader(BaseGeometry *geometry);
 
     void PrintSelf(std::ostream &os, itk::Indent indent) const override;
 
 protected:
 
     FiberBundle( vtkPolyData* fiberPolyData = nullptr );
     ~FiberBundle() override;
 
     void                            GenerateFiberIds();
     void                            UpdateFiberGeometry();
 
 private:
 
     // actual fiber container
     vtkSmartPointer<vtkPolyData>  m_FiberPolyData;
 
     // contains fiber ids
     vtkSmartPointer<vtkDataSet>   m_FiberIdDataSet;
 
     unsigned int m_NumFibers;
 
     vtkSmartPointer<vtkUnsignedCharArray> m_FiberColors;
     vtkSmartPointer<vtkFloatArray> m_FiberWeights;
     std::vector< float > m_FiberLengths;
     float   m_MinFiberLength;
     float   m_MaxFiberLength;
     float   m_MeanFiberLength;
     float   m_MedianFiberLength;
     float   m_LengthStDev;
     itk::TimeStamp m_UpdateTime2D;
     itk::TimeStamp m_UpdateTime3D;
 
     TrackVis_header     m_TrackVisHeader;
 };
 
 } // namespace mitk
 
 #endif /*  _MITK_FiberBundle_H */
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
index 1b4e8a5..8462ed4 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
@@ -1,10 +1,10 @@
 # The project name must correspond to the directory name of your plug-in
 # and must not contain periods.
 project(org_mitk_gui_qt_diffusionimaging_fiberprocessing)
 
 mitk_create_plugin(
   SUBPROJECTS MITK-Diffusion
   EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERPROCESSING_EXPORT
   EXPORTED_INCLUDE_SUFFIXES src
-  MODULE_DEPENDS MitkFiberTracking MitkMriSimulation MitkChart MitkMultilabel
+  MODULE_DEPENDS MitkFiberTracking MitkMriSimulation MitkChart MitkMultilabel MitkModelFit
 )
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
index 8b6b3ac..04dc520 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
@@ -1,1887 +1,1887 @@
 /*===================================================================
 
 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.
 
 ===================================================================*/
 
 
 // Blueberry
 #include <berryISelectionService.h>
 #include <berryIWorkbenchPart.h>
 #include <berryIWorkbenchWindow.h>
 
 // Qmitk
 #include "QmitkFiberProcessingView.h"
 
 #include <QMessageBox>
 
 #include <mitkNodePredicateProperty.h>
 #include <mitkImageCast.h>
 #include <mitkPointSet.h>
 #include <mitkPlanarCircle.h>
 #include <mitkPlanarPolygon.h>
 #include <mitkPlanarRectangle.h>
 #include <mitkPlanarFigureInteractor.h>
 #include <mitkImageAccessByItk.h>
 #include <mitkDataNodeObject.h>
 #include <mitkTensorImage.h>
 #include "usModuleRegistry.h"
 #include <itkFiberCurvatureFilter.h>
 
 #include "mitkNodePredicateDataType.h"
 #include <mitkNodePredicateProperty.h>
 #include <mitkNodePredicateAnd.h>
 #include <mitkNodePredicateNot.h>
 #include <mitkNodePredicateOr.h>
 
 #include <itkResampleImageFilter.h>
 #include <itkGaussianInterpolateImageFunction.h>
 #include <itkImageRegionIteratorWithIndex.h>
 #include <itkTractsToFiberEndingsImageFilter.h>
 #include <itkTractDensityImageFilter.h>
 #include <itkImageRegion.h>
 #include <itkTractsToRgbaImageFilter.h>
 #include <itkFiberExtractionFilter.h>
 
 #include <boost/algorithm/string.hpp>
 #include <boost/lexical_cast.hpp>
 
 const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing";
 const std::string id_DataManager = "org.mitk.views.datamanager";
 using namespace mitk;
 
 QmitkFiberProcessingView::QmitkFiberProcessingView()
   : QmitkAbstractView()
   , m_Controls( 0 )
   , m_CircleCounter(0)
   , m_PolygonCounter(0)
   , m_UpsamplingFactor(1)
 {
 
 }
 
 // Destructor
 QmitkFiberProcessingView::~QmitkFiberProcessingView()
 {
   RemoveObservers();
 }
 
 void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent )
 {
   // build up qt view, unless already done
   if ( !m_Controls )
   {
     // create GUI widgets from the Qt Designer's .ui file
     m_Controls = new Ui::QmitkFiberProcessingViewControls;
     m_Controls->setupUi( parent );
 
     connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) );
     connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) );
     connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) );
     connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) );
     connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) );
     connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) );
 
     connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) );
     connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubtractBundles()) );
     connect(m_Controls->m_CopyBundle, SIGNAL(clicked()), this, SLOT(CopyBundles()) );
 
     connect(m_Controls->m_ExtractFibersButton, SIGNAL(clicked()), this, SLOT(Extract()));
     connect(m_Controls->m_RemoveButton, SIGNAL(clicked()), this, SLOT(Remove()));
     connect(m_Controls->m_ModifyButton, SIGNAL(clicked()), this, SLOT(Modify()));
 
     connect(m_Controls->m_ExtractionMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
     connect(m_Controls->m_RemovalMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
     connect(m_Controls->m_ModificationMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
     connect(m_Controls->m_ExtractionBoxMask, SIGNAL(currentIndexChanged(int)), this, SLOT(OnMaskExtractionChanged()));
 
     m_Controls->m_ColorMapBox->SetDataStorage(this->GetDataStorage());
     mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
     mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
     mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
     mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage");
     mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti);
     isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf);
     mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage);
     mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage);
     m_Controls->m_ColorMapBox->SetPredicate(finalPredicate);
   }
 
   UpdateGui();
   OnMaskExtractionChanged();
 }
 
 void QmitkFiberProcessingView::OnMaskExtractionChanged()
 {
   m_Controls->m_FiberExtractionFractionLabel->setVisible(false);
   m_Controls->m_FiberExtractionFractionBox->setVisible(false);
 
   m_Controls->m_FiberExtractionThresholdLabel->setVisible(false);
   m_Controls->m_FiberExtractionThresholdBox->setVisible(false);
 
   m_Controls->m_InterpolateRoiBox->setVisible(false);
   m_Controls->m_BothEnds->setVisible(false);
 
   m_Controls->m_LabelsBox->setVisible(false);
   m_Controls->m_LabelsLabel->setVisible(false);
 
   if (m_Controls->m_ExtractionBoxMask->currentIndex() == 2 || m_Controls->m_ExtractionBoxMask->currentIndex() == 3)
   {
     m_Controls->m_FiberExtractionFractionLabel->setVisible(true);
     m_Controls->m_FiberExtractionFractionBox->setVisible(true);
 
     m_Controls->m_FiberExtractionThresholdLabel->setVisible(true);
     m_Controls->m_FiberExtractionThresholdBox->setVisible(true);
 
     m_Controls->m_InterpolateRoiBox->setVisible(true);
   }
   else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 0 || m_Controls->m_ExtractionBoxMask->currentIndex() == 1)
   {
     if (m_Controls->m_ExtractionBoxMask->currentIndex() != 3)
       m_Controls->m_BothEnds->setVisible(true);
     m_Controls->m_InterpolateRoiBox->setVisible(true);
 
     m_Controls->m_FiberExtractionThresholdLabel->setVisible(true);
     m_Controls->m_FiberExtractionThresholdBox->setVisible(true);
   }
   else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 4)
   {
     m_Controls->m_BothEnds->setVisible(true);
 
     m_Controls->m_LabelsBox->setVisible(true);
     m_Controls->m_LabelsLabel->setVisible(true);
   }
 }
 
 void QmitkFiberProcessingView::SetFocus()
 {
   m_Controls->toolBoxx->setFocus();
 }
 
 void QmitkFiberProcessingView::Modify()
 {
   switch (m_Controls->m_ModificationMethodBox->currentIndex())
   {
   case 0:
   {
     ResampleSelectedBundlesSpline();
     break;
   }
   case 1:
   {
     ResampleSelectedBundlesLinear();
     break;
   }
   case 2:
   {
     CompressSelectedBundles();
     break;
   }
   case 3:
   {
     MirrorFibers();
     break;
   }
   case 4:
   {
     WeightFibers();
     break;
   }
   case 5:
   {
     DoWeightColorCoding();
     break;
   }
   case 6:
   {
     DoCurvatureColorCoding();
     break;
   }
   case 7:
   {
     DoLengthColorCoding();
     break;
   }
   case 8:
   {
     DoImageColorCoding();
     break;
   }
   }
 }
 
 void QmitkFiberProcessingView::WeightFibers()
 {
   float weight = this->m_Controls->m_BundleWeightBox->value();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     fib->SetFiberWeights(weight);
   }
 
 }
 
 void QmitkFiberProcessingView::Remove()
 {
   switch (m_Controls->m_RemovalMethodBox->currentIndex())
   {
   case 0:
   {
     RemoveDir();
     break;
   }
   case 1:
   {
     PruneBundle();
     break;
   }
   case 2:
   {
     ApplyCurvatureThreshold();
     break;
   }
   case 3:
   {
     RemoveWithMask(false);
     break;
   }
   case 4:
   {
     RemoveWithMask(true);
     break;
   }
   case 5:
   {
     ApplyWeightThreshold();
     break;
   }
   case 6:
   {
     ApplyDensityThreshold();
     break;
   }
   }
 }
 
 void QmitkFiberProcessingView::Extract()
 {
   switch (m_Controls->m_ExtractionMethodBox->currentIndex())
   {
   case 0:
   {
     ExtractWithPlanarFigure();
     break;
   }
   case 1:
   {
     switch (m_Controls->m_ExtractionBoxMask->currentIndex())
     {
     {
     case 0:
         ExtractWithMask(true, false, false);
         break;
     }
     {
     case 1:
         ExtractWithMask(true, true, false);
         break;
     }
     {
     case 2:
         ExtractWithMask(false, false, false);
         break;
     }
     {
     case 3:
         ExtractWithMask(false, true, false);
         break;
     }
     {
     case 4:
         ExtractWithMask(true, false, true);
         break;
     }
     }
     break;
   }
   }
 }
 
 void QmitkFiberProcessingView::PruneBundle()
 {
   int minLength = this->m_Controls->m_PruneFibersMinBox->value();
   int maxLength = this->m_Controls->m_PruneFibersMaxBox->value();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     if (!fib->RemoveShortFibers(minLength))
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
     else if (!fib->RemoveLongFibers(maxLength))
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::ApplyWeightThreshold()
 {
   float thr = this->m_Controls->m_WeightThresholdBox->value();
   std::vector< DataNode::Pointer > nodes = m_SelectedFB;
   for (auto node : nodes)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     mitk::FiberBundle::Pointer newFib = fib->FilterByWeights(thr);
     if (newFib->GetNumFibers()>0)
     {
       switch(m_Controls->m_LookupTableTypeBox->currentIndex())
       {
       case 0:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::JET);
         break;
       case 1:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::HOT_IRON);
         break;
       case 2:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::PLASMA);
         break;
       case 3:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::INFERNO);
         break;
       case 4:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::VIRIDIS);
         break;
       case 5:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::MAGMA);
         break;
       case 6:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::GRAYSCALE);
         break;
       case 7:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::MULTILABEL);
         break;
       default:
         newFib->ColorFibersByFiberWeights(false, mitk::LookupTable::JET);
       }
 
       node->SetData(newFib);
     }
     else
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::ApplyDensityThreshold()
 {
   float thr = this->m_Controls->m_DensityThresholdBox->value();
   float ol = this->m_Controls->m_DensityOverlapBox->value();
   std::vector< DataNode::Pointer > nodes = m_SelectedFB;
   for (auto node : nodes)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     itk::TractDensityImageFilter< ItkFloatImageType >::Pointer generator = itk::TractDensityImageFilter< ItkFloatImageType >::New();
     generator->SetFiberBundle(fib);
     generator->SetMode(TDI_MODE::DENSITY);
     generator->SetOutputAbsoluteValues(false);
     generator->Update();
 
     itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
     extractor->SetRoiImages({generator->GetOutput()});
     extractor->SetInputFiberBundle(fib);
     extractor->SetOverlapFraction(ol);
     extractor->SetInterpolate(true);
     extractor->SetThreshold(thr);
     extractor->SetNoNegatives(true);
     extractor->Update();
 
     if (extractor->GetPositives().empty())
     {
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
       continue;
     }
 
     mitk::FiberBundle::Pointer newFib = extractor->GetPositives().at(0);
     if (newFib->GetNumFibers()>0)
       node->SetData(newFib);
     else
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::ApplyCurvatureThreshold()
 {
   int angle = this->m_Controls->m_CurvSpinBox->value();
   int dist = this->m_Controls->m_CurvDistanceSpinBox->value();
   std::vector< DataNode::Pointer > nodes = m_SelectedFB;
   for (auto node : nodes)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     itk::FiberCurvatureFilter::Pointer filter = itk::FiberCurvatureFilter::New();
     filter->SetInputFiberBundle(fib);
     filter->SetAngularDeviation(angle);
     filter->SetDistance(dist);
     filter->SetRemoveFibers(m_Controls->m_RemoveCurvedFibersBox->isChecked());
     filter->Update();
     mitk::FiberBundle::Pointer newFib = filter->GetOutputFiberBundle();
     if (newFib->GetNumFibers()>0)
     {
       newFib->ColorFibersByOrientation();
       node->SetData(newFib);
     }
     else
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::RemoveDir()
 {
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     vnl_vector_fixed<double,3> dir;
     dir[0] = m_Controls->m_ExtractDirX->value();
     dir[1] = m_Controls->m_ExtractDirY->value();
     dir[2] = m_Controls->m_ExtractDirZ->value();
     fib->RemoveDir(dir,cos((float)m_Controls->m_ExtractAngle->value()*itk::Math::pi/180));
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::RemoveWithMask(bool removeInside)
 {
   if (m_RoiImageNode.IsNull())
     return;
 
   mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_RoiImageNode->GetData());
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
     mitk::CastToItkImage(mitkMask, mask);
     mitk::FiberBundle::Pointer newFib = fib->RemoveFibersOutside(mask, removeInside);
     if (newFib->GetNumFibers()<=0)
     {
       QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
       continue;
     }
     node->SetData(newFib);
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::ExtractWithMask(bool onlyEnds, bool invert, bool labelmap)
 {
   if (m_RoiImageNode.IsNull())
     return;
 
   mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_RoiImageNode->GetData());
   for (auto node : m_SelectedFB)
   {
     std::string roi_name = m_RoiImageNode->GetName();
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
     mitk::CastToItkImage(mitkMask, mask);
 
     itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
     extractor->SetInputFiberBundle(fib);
     extractor->SetRoiImages({mask});
     extractor->SetRoiImageNames({roi_name});
     extractor->SetThreshold(m_Controls->m_FiberExtractionThresholdBox->value());
     extractor->SetOverlapFraction(m_Controls->m_FiberExtractionFractionBox->value());
     extractor->SetBothEnds(m_Controls->m_BothEnds->isChecked());
     extractor->SetInterpolate(m_Controls->m_InterpolateRoiBox->isChecked());
     extractor->SetMinFibersPerTract(m_Controls->m_MinExtractedFibersBox->value());
     extractor->SetSplitByRoi(true);
     if (invert)
       extractor->SetNoPositives(true);
     else
       extractor->SetNoNegatives(true);
 
     if (labelmap)
     {
       std::string labels_string = m_Controls->m_LabelsBox->text().toStdString();
       if (labels_string!="ALL")
       {
         std::vector<std::string> strs;
         boost::split(strs,labels_string,boost::is_any_of(" ,;\t"));
 
         std::vector< unsigned short > labels_vector;
         for (auto v : strs)
         {
           try{
             unsigned short l = boost::lexical_cast<unsigned short>(v);
             labels_vector.push_back(l);
           }
           catch(...)
           {
 
           }
         }
         extractor->SetLabels(labels_vector);
       }
 
       extractor->SetInterpolate(false);
       extractor->SetInputType(itk::FiberExtractionFilter<float>::INPUT::LABEL_MAP);
       extractor->SetSplitLabels(true);
       onlyEnds = true;
     }
 
     if (onlyEnds)
       extractor->SetMode(itk::FiberExtractionFilter<float>::MODE::ENDPOINTS);
     extractor->Update();
 
     std::vector< mitk::FiberBundle::Pointer > newFibs;
     if (invert)
       newFibs = extractor->GetNegatives();
     else
       newFibs = extractor->GetPositives();
 
     if (newFibs.empty())
     {
       QMessageBox::information(nullptr, "No output generated:", "No fibers could be extracted.");
       continue;
     }
 
     auto labels = extractor->GetPositiveLabels();
     for (unsigned int i=0; i<newFibs.size(); ++i)
     {
       DataNode::Pointer newNode = DataNode::New();
       auto fib = newFibs.at(i);
 
       newNode->SetData(fib);
       std::string name = roi_name;
       if (i<labels.size())
         name = labels.at(i);
 
       if (invert)
       {
         if (onlyEnds)
           name = "not-ending-in-" + name;
         else
           name = "not-passing-" + name;
       }
       else if (!labelmap)
       {
         if (onlyEnds)
           name = "ending-in-" + name;
         else
           name = "passing-" + name;
       }
 
       float currentThickness = 0;
       node->GetFloatProperty("Fiber2DSliceThickness", currentThickness);
       newNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(currentThickness));
 
       GetDataStorage()->Add(newNode, node);
     }
     node->SetVisibility(false);
   }
 }
 
 void QmitkFiberProcessingView::GenerateRoiImage()
 {
   if (m_SelectedPF.empty())
     return;
 
   mitk::BaseGeometry::Pointer geometry;
   if (!m_SelectedFB.empty())
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.front()->GetData());
     geometry = fib->GetGeometry();
   }
   else if (m_SelectedImage)
     geometry = m_SelectedImage->GetGeometry();
   else
     return;
 
   itk::Vector<double,3> spacing = geometry->GetSpacing();
   spacing /= m_UpsamplingFactor;
 
   mitk::Point3D newOrigin = geometry->GetOrigin();
   mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
   newOrigin[0] += bounds.GetElement(0);
   newOrigin[1] += bounds.GetElement(2);
   newOrigin[2] += bounds.GetElement(4);
 
   itk::Matrix<double, 3, 3> direction;
   itk::ImageRegion<3> imageRegion;
   for (int i=0; i<3; i++)
     for (int j=0; j<3; j++)
       direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j];
   imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
   imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
   imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
 
   m_PlanarFigureImage = ItkUCharImageType::New();
   m_PlanarFigureImage->SetSpacing( spacing );   // Set the image spacing
   m_PlanarFigureImage->SetOrigin( newOrigin );     // Set the image origin
   m_PlanarFigureImage->SetDirection( direction );  // Set the image direction
   m_PlanarFigureImage->SetRegions( imageRegion );
   m_PlanarFigureImage->Allocate();
   m_PlanarFigureImage->FillBuffer( 0 );
 
   Image::Pointer tmpImage = Image::New();
   tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
   tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
 
   std::string name = m_SelectedPF.at(0)->GetName();
   WritePfToImage(m_SelectedPF.at(0), tmpImage);
   for (unsigned int i=1; i<m_SelectedPF.size(); i++)
   {
     name += "+";
     name += m_SelectedPF.at(i)->GetName();
     WritePfToImage(m_SelectedPF.at(i), tmpImage);
   }
 
   DataNode::Pointer node = DataNode::New();
   tmpImage = Image::New();
   tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
   tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
   node->SetData(tmpImage);
   node->SetName(name);
   this->GetDataStorage()->Add(node);
 }
 
 void QmitkFiberProcessingView::WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image)
 {
   if (dynamic_cast<mitk::PlanarFigure*>(node->GetData()))
   {
     m_PlanarFigure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
     AccessFixedDimensionByItk_2(
           image,
           InternalReorientImagePlane, 3,
           m_PlanarFigure->GetGeometry(), -1);
 
     AccessFixedDimensionByItk_2(
           m_InternalImage,
           InternalCalculateMaskFromPlanarFigure,
           3, 2, node->GetName() );
   }
   else if (dynamic_cast<mitk::PlanarFigureComposite*>(node->GetData()))
   {
     DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(node);
     for (unsigned int i=0; i<children->Size(); i++)
     {
       WritePfToImage(children->at(i), image);
     }
   }
 }
 
 template < typename TPixel, unsigned int VImageDimension >
 void QmitkFiberProcessingView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* planegeo3D, int additionalIndex )
 {
   typedef itk::Image< TPixel, VImageDimension > ImageType;
   typedef itk::Image< float, VImageDimension > FloatImageType;
 
   typedef itk::ResampleImageFilter<ImageType, FloatImageType, double> ResamplerType;
   typename ResamplerType::Pointer resampler = ResamplerType::New();
 
   mitk::PlaneGeometry* planegeo = dynamic_cast<mitk::PlaneGeometry*>(planegeo3D);
 
   float upsamp = m_UpsamplingFactor;
   float gausssigma = 0.5;
 
   // Spacing
   typename ResamplerType::SpacingType spacing = planegeo->GetSpacing();
   spacing[0] = image->GetSpacing()[0] / upsamp;
   spacing[1] = image->GetSpacing()[1] / upsamp;
   spacing[2] = image->GetSpacing()[2];
   resampler->SetOutputSpacing( spacing );
 
   // Size
   typename ResamplerType::SizeType size;
   size[0] = planegeo->GetExtentInMM(0) / spacing[0];
   size[1] = planegeo->GetExtentInMM(1) / spacing[1];
   size[2] = 1;
   resampler->SetSize( size );
 
   // Origin
   typename mitk::Point3D orig = planegeo->GetOrigin();
   typename mitk::Point3D corrorig;
   planegeo3D->WorldToIndex(orig,corrorig);
   corrorig[0] += 0.5/upsamp;
   corrorig[1] += 0.5/upsamp;
   corrorig[2] += 0;
   planegeo3D->IndexToWorld(corrorig,corrorig);
   resampler->SetOutputOrigin(corrorig );
 
   // Direction
   typename ResamplerType::DirectionType direction;
   typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix();
   for(unsigned int c=0; c<matrix.ColumnDimensions; c++)
   {
     double sum = 0;
     for(unsigned int r=0; r<matrix.RowDimensions; r++)
       sum += matrix(r,c)*matrix(r,c);
     for(unsigned int r=0; r<matrix.RowDimensions; r++)
       direction(r,c) = matrix(r,c)/sqrt(sum);
   }
   resampler->SetOutputDirection( direction );
 
   // Gaussian interpolation
   if(gausssigma != 0)
   {
     double sigma[3];
     for( unsigned int d = 0; d < 3; d++ )
       sigma[d] = gausssigma * image->GetSpacing()[d];
     double alpha = 2.0;
     typedef itk::GaussianInterpolateImageFunction<ImageType, double> GaussianInterpolatorType;
     typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New();
     interpolator->SetInputImage( image );
     interpolator->SetParameters( sigma, alpha );
     resampler->SetInterpolator( interpolator );
   }
   else
   {
     typedef typename itk::LinearInterpolateImageFunction<ImageType, double> InterpolatorType;
     typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
     interpolator->SetInputImage( image );
     resampler->SetInterpolator( interpolator );
   }
 
   resampler->SetInput( image );
   resampler->SetDefaultPixelValue(0);
   resampler->Update();
 
   if(additionalIndex < 0)
   {
     this->m_InternalImage = mitk::Image::New();
     this->m_InternalImage->InitializeByItk( resampler->GetOutput() );
     this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() );
   }
 }
 
 template < typename TPixel, unsigned int VImageDimension >
 void QmitkFiberProcessingView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string )
 {
   typedef itk::Image< TPixel, VImageDimension > ImageType;
 
   // Generate mask image as new image with same header as input image and
   // initialize with "1".
   ItkUCharImageType::Pointer newMaskImage = ItkUCharImageType::New();
   newMaskImage->SetSpacing( image->GetSpacing() );   // Set the image spacing
   newMaskImage->SetOrigin( image->GetOrigin() );     // Set the image origin
   newMaskImage->SetDirection( image->GetDirection() );  // Set the image direction
   newMaskImage->SetRegions( image->GetLargestPossibleRegion() );
   newMaskImage->Allocate();
   newMaskImage->FillBuffer( 1 );
 
   // Generate VTK polygon from (closed) PlanarFigure polyline
   // (The polyline points are shifted by -0.5 in z-direction to make sure
   // that the extrusion filter, which afterwards elevates all points by +0.5
   // in z-direction, creates a 3D object which is cut by the the plane z=0)
   const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry();
   const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 );
   const BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 );
 
   vtkPolyData *polyline = vtkPolyData::New();
   polyline->Allocate( 1, 1 );
 
   // Determine x- and y-dimensions depending on principal axis
   int i0, i1;
   switch ( axis )
   {
   case 0:
     i0 = 1;
     i1 = 2;
     break;
   case 1:
     i0 = 0;
     i1 = 2;
     break;
   case 2:
   default:
     i0 = 0;
     i1 = 1;
     break;
   }
 
   // Create VTK polydata object of polyline contour
   vtkPoints *points = vtkPoints::New();
   PlanarFigure::PolyLineType::const_iterator it;
   unsigned int numberOfPoints = 0;
 
   for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it )
   {
     Point3D point3D;
 
     // Convert 2D point back to the local index coordinates of the selected image
     Point2D point2D = *it;
     planarFigurePlaneGeometry->WorldToIndex(point2D, point2D);
     point2D[0] -= 0.5/m_UpsamplingFactor;
     point2D[1] -= 0.5/m_UpsamplingFactor;
     planarFigurePlaneGeometry->IndexToWorld(point2D, point2D);
     planarFigurePlaneGeometry->Map( point2D, point3D );
 
     // Polygons (partially) outside of the image bounds can not be processed further due to a bug in vtkPolyDataToImageStencil
     if ( !imageGeometry3D->IsInside( point3D ) )
     {
       float bounds[2] = {0,0};
       bounds[0] =
           this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0);
       bounds[1] =
           this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1);
 
       imageGeometry3D->WorldToIndex( point3D, point3D );
 
       if (point3D[i0]<0)
         point3D[i0] = 0.0;
       else if (point3D[i0]>bounds[0])
         point3D[i0] = bounds[0]-0.001;
 
       if (point3D[i1]<0)
         point3D[i1] = 0.0;
       else if (point3D[i1]>bounds[1])
         point3D[i1] = bounds[1]-0.001;
 
       points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
       numberOfPoints++;
     }
     else
     {
       imageGeometry3D->WorldToIndex( point3D, point3D );
       // Add point to polyline array
       points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
       numberOfPoints++;
     }
   }
   polyline->SetPoints( points );
   points->Delete();
 
   vtkIdType *ptIds = new vtkIdType[numberOfPoints];
   for ( vtkIdType i = 0; i < numberOfPoints; ++i )
     ptIds[i] = i;
   polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds );
 
   // Extrude the generated contour polygon
   vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New();
   extrudeFilter->SetInputData( polyline );
   extrudeFilter->SetScaleFactor( 1 );
   extrudeFilter->SetExtrusionTypeToNormalExtrusion();
   extrudeFilter->SetVector( 0.0, 0.0, 1.0 );
 
   // Make a stencil from the extruded polygon
   vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New();
   polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() );
 
   // Export from ITK to VTK (to use a VTK filter)
   typedef itk::VTKImageImport< ItkUCharImageType > ImageImportType;
   typedef itk::VTKImageExport< ItkUCharImageType > ImageExportType;
 
   typename ImageExportType::Pointer itkExporter = ImageExportType::New();
   itkExporter->SetInput( newMaskImage );
 
   vtkImageImport *vtkImporter = vtkImageImport::New();
   this->ConnectPipelines( itkExporter, vtkImporter );
   vtkImporter->Update();
 
   // Apply the generated image stencil to the input image
   vtkImageStencil *imageStencilFilter = vtkImageStencil::New();
   imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() );
   imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() );
   imageStencilFilter->ReverseStencilOff();
   imageStencilFilter->SetBackgroundValue( 0 );
   imageStencilFilter->Update();
 
   // Export from VTK back to ITK
   vtkImageExport *vtkExporter = vtkImageExport::New();
   vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() );
   vtkExporter->Update();
 
   typename ImageImportType::Pointer itkImporter = ImageImportType::New();
   this->ConnectPipelines( vtkExporter, itkImporter );
   itkImporter->Update();
 
   // calculate cropping bounding box
   m_InternalImageMask3D = itkImporter->GetOutput();
   m_InternalImageMask3D->SetDirection(image->GetDirection());
 
   itk::ImageRegionConstIterator<ItkUCharImageType>
       itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion());
   itk::ImageRegionIterator<ImageType>
       itimage(image, image->GetLargestPossibleRegion());
 
   itmask.GoToBegin();
   itimage.GoToBegin();
 
   typename ImageType::SizeType lowersize = {{itk::NumericTraits<unsigned long>::max(),itk::NumericTraits<unsigned long>::max(),itk::NumericTraits<unsigned long>::max()}};
   typename ImageType::SizeType uppersize = {{0,0,0}};
   while( !itmask.IsAtEnd() )
   {
     if(itmask.Get() == 0)
       itimage.Set(0);
     else
     {
       typename ImageType::IndexType index = itimage.GetIndex();
       typename ImageType::SizeType signedindex;
       signedindex[0] = index[0];
       signedindex[1] = index[1];
       signedindex[2] = index[2];
 
       lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0];
       lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1];
       lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2];
 
       uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0];
       uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1];
       uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2];
     }
 
     ++itmask;
     ++itimage;
   }
 
   typename ImageType::IndexType index;
   index[0] = lowersize[0];
   index[1] = lowersize[1];
   index[2] = lowersize[2];
 
   typename ImageType::SizeType size;
   size[0] = uppersize[0] - lowersize[0] + 1;
   size[1] = uppersize[1] - lowersize[1] + 1;
   size[2] = uppersize[2] - lowersize[2] + 1;
 
   itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size);
 
   // crop internal mask
   typedef itk::RegionOfInterestImageFilter< ItkUCharImageType, ItkUCharImageType > ROIMaskFilterType;
   typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New();
   roi2->SetRegionOfInterest(cropRegion);
   roi2->SetInput(m_InternalImageMask3D);
   roi2->Update();
   m_InternalImageMask3D = roi2->GetOutput();
 
   Image::Pointer tmpImage = Image::New();
   tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer());
   tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer());
 
   Image::Pointer tmpImage2 = Image::New();
   tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer());
   const BaseGeometry *pfImageGeometry3D = tmpImage2->GetGeometry( 0 );
 
   const BaseGeometry *intImageGeometry3D = tmpImage->GetGeometry( 0 );
 
   typedef itk::ImageRegionIteratorWithIndex<ItkUCharImageType> IteratorType;
   IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion());
   imageIterator.GoToBegin();
   while ( !imageIterator.IsAtEnd() )
   {
     unsigned char val = imageIterator.Value();
     if (val>0)
     {
       itk::Index<3> index = imageIterator.GetIndex();
       Point3D point;
       point[0] = index[0];
       point[1] = index[1];
       point[2] = index[2];
 
       intImageGeometry3D->IndexToWorld(point, point);
       pfImageGeometry3D->WorldToIndex(point, point);
 
       point[i0] += 0.5;
       point[i1] += 0.5;
 
       index[0] = point[0];
       index[1] = point[1];
       index[2] = point[2];
 
       if (pfImageGeometry3D->IsIndexInside(index))
         m_PlanarFigureImage->SetPixel(index, 1);
     }
     ++imageIterator;
   }
 
   // Clean up VTK objects
   polyline->Delete();
   extrudeFilter->Delete();
   polyDataToImageStencil->Delete();
   vtkImporter->Delete();
   imageStencilFilter->Delete();
   //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak??
   delete[] ptIds;
 }
 
 void QmitkFiberProcessingView::UpdateGui()
 {
   m_Controls->m_FibLabel->setText("<font color='red'>mandatory</font>");
   m_Controls->m_PfLabel->setText("<font color='grey'>needed for extraction</font>");
   m_Controls->m_InputData->setTitle("Please Select Input Data");
 
   m_Controls->m_RemoveButton->setEnabled(false);
 
   m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false);
   m_Controls->PFCompoANDButton->setEnabled(false);
   m_Controls->PFCompoORButton->setEnabled(false);
   m_Controls->PFCompoNOTButton->setEnabled(false);
 
   m_Controls->m_GenerateRoiImage->setEnabled(false);
   m_Controls->m_ExtractFibersButton->setEnabled(false);
   m_Controls->m_ModifyButton->setEnabled(false);
 
   m_Controls->m_CopyBundle->setEnabled(false);
   m_Controls->m_JoinBundles->setEnabled(false);
   m_Controls->m_SubstractBundles->setEnabled(false);
 
   // disable alle frames
   m_Controls->m_BundleWeightFrame->setVisible(false);
   m_Controls->m_ExtactionFramePF->setVisible(false);
   m_Controls->m_RemoveDirectionFrame->setVisible(false);
   m_Controls->m_RemoveLengthFrame->setVisible(false);
   m_Controls->m_RemoveCurvatureFrame->setVisible(false);
   m_Controls->m_RemoveByWeightFrame->setVisible(false);
   m_Controls->m_RemoveByDensityFrame->setVisible(false);
   m_Controls->m_SmoothFibersFrame->setVisible(false);
   m_Controls->m_CompressFibersFrame->setVisible(false);
   m_Controls->m_ColorFibersFrame->setVisible(false);
   m_Controls->m_MirrorFibersFrame->setVisible(false);
   m_Controls->m_MaskExtractionFrame->setVisible(false);
   m_Controls->m_ColorMapBox->setVisible(false);
   m_Controls->m_ValueAsWeightBox->setVisible(false);
 
   bool pfSelected = !m_SelectedPF.empty();
   bool fibSelected = !m_SelectedFB.empty();
   bool multipleFibsSelected = (m_SelectedFB.size()>1);
   bool maskSelected = m_RoiImageNode.IsNotNull();
   bool imageSelected = m_SelectedImage.IsNotNull();
 
   // toggle visibility of elements according to selected method
   switch ( m_Controls->m_ExtractionMethodBox->currentIndex() )
   {
   case 0:
     m_Controls->m_ExtactionFramePF->setVisible(true);
     break;
   case 1:
     m_Controls->m_MaskExtractionFrame->setVisible(true);
     break;
   }
 
   switch ( m_Controls->m_RemovalMethodBox->currentIndex() )
   {
   case 0:
     m_Controls->m_RemoveDirectionFrame->setVisible(true);
     if ( fibSelected )
       m_Controls->m_RemoveButton->setEnabled(true);
     break;
   case 1:
     m_Controls->m_RemoveLengthFrame->setVisible(true);
     if ( fibSelected )
       m_Controls->m_RemoveButton->setEnabled(true);
     break;
   case 2:
     m_Controls->m_RemoveCurvatureFrame->setVisible(true);
     if ( fibSelected )
       m_Controls->m_RemoveButton->setEnabled(true);
     break;
   case 3:
     break;
   case 4:
     break;
   case 5:
     m_Controls->m_RemoveByWeightFrame->setVisible(true);
     if ( fibSelected )
       m_Controls->m_RemoveButton->setEnabled(true);
     break;
   case 6:
     m_Controls->m_RemoveByDensityFrame->setVisible(true);
     if ( fibSelected )
       m_Controls->m_RemoveButton->setEnabled(true);
     break;
   }
 
   switch ( m_Controls->m_ModificationMethodBox->currentIndex() )
   {
   case 0:
     m_Controls->m_SmoothFibersFrame->setVisible(true);
     break;
   case 1:
     m_Controls->m_SmoothFibersFrame->setVisible(true);
     break;
   case 2:
     m_Controls->m_CompressFibersFrame->setVisible(true);
     break;
   case 3:
     m_Controls->m_MirrorFibersFrame->setVisible(true);
     if (m_SelectedSurfaces.size()>0)
       m_Controls->m_ModifyButton->setEnabled(true);
     break;
   case 4:
     m_Controls->m_BundleWeightFrame->setVisible(true);
     break;
   case 5:
     m_Controls->m_ColorFibersFrame->setVisible(true);
     break;
   case 6:
     m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
     break;
   case 7:
     m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
     break;
   case 8:
     m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
     m_Controls->m_ColorMapBox->setVisible(true);
     break;
   }
 
   // are fiber bundles selected?
   if ( fibSelected )
   {
     m_Controls->m_CopyBundle->setEnabled(true);
     m_Controls->m_ModifyButton->setEnabled(true);
     m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
     m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str()));
 
     // one bundle and one planar figure needed to extract fibers
     if (pfSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==0)
     {
       m_Controls->m_InputData->setTitle("Input Data");
       m_Controls->m_PfLabel->setText(QString(m_SelectedPF.at(0)->GetName().c_str()));
       m_Controls->m_ExtractFibersButton->setEnabled(true);
     }
 
     // more than two bundles needed to join/subtract
     if (multipleFibsSelected)
     {
       m_Controls->m_FibLabel->setText("multiple bundles selected");
 
       m_Controls->m_JoinBundles->setEnabled(true);
       m_Controls->m_SubstractBundles->setEnabled(true);
     }
 
     if (maskSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==1)
     {
       m_Controls->m_InputData->setTitle("Input Data");
       m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str()));
       m_Controls->m_ExtractFibersButton->setEnabled(true);
     }
 
     if (maskSelected && (m_Controls->m_RemovalMethodBox->currentIndex()==3 || m_Controls->m_RemovalMethodBox->currentIndex()==4) )
     {
       m_Controls->m_InputData->setTitle("Input Data");
       m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str()));
       m_Controls->m_RemoveButton->setEnabled(true);
     }
   }
 
   // are planar figures selected?
   if (pfSelected)
   {
     if ( fibSelected || m_SelectedImage.IsNotNull())
       m_Controls->m_GenerateRoiImage->setEnabled(true);
 
     if (m_SelectedPF.size() > 1)
     {
       m_Controls->PFCompoANDButton->setEnabled(true);
       m_Controls->PFCompoORButton->setEnabled(true);
     }
     else
       m_Controls->PFCompoNOTButton->setEnabled(true);
   }
 
   // is image selected
   if (imageSelected || maskSelected)
   {
     m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
   }
 }
 
 void QmitkFiberProcessingView::NodeRemoved(const mitk::DataNode* node )
 {
   for (auto fnode: m_SelectedFB)
     if (node == fnode)
     {
       m_SelectedFB.clear();
       break;
     }
 
   berry::IWorkbenchPart::Pointer nullPart;
   QList<mitk::DataNode::Pointer> nodes;
   OnSelectionChanged(nullPart, nodes);
 }
 
 void QmitkFiberProcessingView::NodeAdded(const mitk::DataNode* )
 {
   if (!m_Controls->m_InteractiveBox->isChecked())
   {
     berry::IWorkbenchPart::Pointer nullPart;
     QList<mitk::DataNode::Pointer> nodes;
     OnSelectionChanged(nullPart, nodes);
   }
 }
 
 void QmitkFiberProcessingView::OnEndInteraction()
 {
   if (m_Controls->m_InteractiveBox->isChecked())
     ExtractWithPlanarFigure(true);
 }
 
 void QmitkFiberProcessingView::AddObservers()
 {
   typedef itk::SimpleMemberCommand< QmitkFiberProcessingView > SimpleCommandType;
   for (auto node : m_SelectedPF)
   {
     mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
     if (figure!=nullptr)
     {
       figure->RemoveAllObservers();
 
       // add observer for event when interaction with figure starts
       SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New();
       endInteractionCommand->SetCallbackFunction( this, &QmitkFiberProcessingView::OnEndInteraction);
       m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand );
     }
   }
 }
 
 void QmitkFiberProcessingView::RemoveObservers()
 {
   for (auto node : m_SelectedPF)
   {
     mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
     if (figure!=nullptr)
       figure->RemoveAllObservers();
   }
 }
 
 void QmitkFiberProcessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes)
 {
   RemoveObservers();
 
   //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection
   std::vector<mitk::DataNode::Pointer>  lastSelectedFB = m_SelectedFB;
   m_SelectedFB.clear();
   m_SelectedPF.clear();
   m_SelectedSurfaces.clear();
   m_SelectedImage = nullptr;
   m_RoiImageNode = nullptr;
 
   for (auto node: nodes)
   {
     if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
       m_SelectedFB.push_back(node);
     else if (dynamic_cast<mitk::PlanarPolygon*>(node->GetData()) || dynamic_cast<mitk::PlanarFigureComposite*>(node->GetData()) || dynamic_cast<mitk::PlanarCircle*>(node->GetData()))
       m_SelectedPF.push_back(node);
     else if (dynamic_cast<mitk::Image*>(node->GetData()))
     {
       m_SelectedImage = dynamic_cast<mitk::Image*>(node->GetData());
       if (m_SelectedImage->GetDimension()==3)
         m_RoiImageNode = node;
     }
     else if (dynamic_cast<mitk::Surface*>(node->GetData()))
       m_SelectedSurfaces.push_back(dynamic_cast<mitk::Surface*>(node->GetData()));
   }
 
   // if we perform interactive fiber extraction, we want to avoid auto-selection of the extracted bundle
   if (m_SelectedFB.empty() && m_Controls->m_InteractiveBox->isChecked())
     m_SelectedFB = lastSelectedFB;
 
   // if no fibers or surfaces are selected, select topmost
   if (m_SelectedFB.empty() && m_SelectedSurfaces.empty())
   {
     int maxLayer = 0;
     itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDataStorage()->GetAll();
     for (unsigned int i=0; i<nodes->Size(); i++)
       if (dynamic_cast<mitk::FiberBundle*>(nodes->at(i)->GetData()))
       {
         mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i));
         if (sources->Size()>0)
           continue;
 
         int layer = 0;
         nodes->at(i)->GetPropertyValue("layer", layer);
         if (layer>=maxLayer)
         {
           maxLayer = layer;
           m_SelectedFB.clear();
           m_SelectedFB.push_back(nodes->at(i));
         }
       }
   }
 
   // if no plar figure is selected, select topmost
   if (m_SelectedPF.empty())
   {
     int maxLayer = 0;
     itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDataStorage()->GetAll();
     for (unsigned int i=0; i<nodes->Size(); i++)
       if (dynamic_cast<mitk::PlanarPolygon*>(nodes->at(i)->GetData()) || dynamic_cast<mitk::PlanarFigureComposite*>(nodes->at(i)->GetData()) || dynamic_cast<mitk::PlanarCircle*>(nodes->at(i)->GetData()))
       {
         mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i));
         if (sources->Size()>0)
           continue;
 
         int layer = 0;
         nodes->at(i)->GetPropertyValue("layer", layer);
         if (layer>=maxLayer)
         {
           maxLayer = layer;
           m_SelectedPF.clear();
           m_SelectedPF.push_back(nodes->at(i));
         }
       }
   }
 
   AddObservers();
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::OnDrawPolygon()
 {
   mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New();
   figure->ClosedOn();
   this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter));
 }
 
 void QmitkFiberProcessingView::OnDrawCircle()
 {
   mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New();
   this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter));
 }
 
 void QmitkFiberProcessingView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *, mitk::BaseProperty* )
 {
   // initialize figure's geometry with empty geometry
   mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New();
   figure->SetPlaneGeometry( emptygeometry );
 
   //set desired data to DataNode where Planarfigure is stored
   mitk::DataNode::Pointer newNode = mitk::DataNode::New();
   newNode->SetName(name.toStdString());
   newNode->SetData(figure);
   newNode->SetBoolProperty("planarfigure.3drendering", true);
   newNode->SetBoolProperty("planarfigure.3drendering.fill", true);
 
   mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(newNode->GetDataInteractor().GetPointer());
   if(figureInteractor.IsNull())
   {
     figureInteractor = mitk::PlanarFigureInteractor::New();
     us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
     figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
     figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
     figureInteractor->SetDataNode(newNode);
   }
 
   // figure drawn on the topmost layer / image
   GetDataStorage()->Add(newNode );
 
   RemoveObservers();
   for(unsigned int i = 0; i < m_SelectedPF.size(); i++)
     m_SelectedPF[i]->SetSelected(false);
 
   newNode->SetSelected(true);
   m_SelectedPF.clear();
   m_SelectedPF.push_back(newNode);
   AddObservers();
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::ExtractWithPlanarFigure(bool interactive)
 {
   if ( m_SelectedFB.empty() || m_SelectedPF.empty() ){
     QMessageBox::information( nullptr, "Warning", "No fibe bundle selected!");
     return;
   }
 
   try
   {
     std::vector<mitk::DataNode::Pointer> fiberBundles = m_SelectedFB;
     mitk::DataNode::Pointer planarFigure = m_SelectedPF.at(0);
     for (unsigned int i=0; i<fiberBundles.size(); i++)
     {
       mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(fiberBundles.at(i)->GetData());
       mitk::FiberBundle::Pointer extFB = fib->ExtractFiberSubset(planarFigure, GetDataStorage());
 
       float currentThickness = 0;
       fiberBundles.at(i)->GetFloatProperty("Fiber2DSliceThickness", currentThickness);
 
       if (interactive && m_Controls->m_InteractiveBox->isChecked())
       {
         if (m_InteractiveNode.IsNull())
         {
 
           m_InteractiveNode = mitk::DataNode::New();
           QString name("Interactive");
           m_InteractiveNode->SetName(name.toStdString());
           m_InteractiveNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(currentThickness));
           GetDataStorage()->Add(m_InteractiveNode);
         }
         float op = 5.0/sqrt(fib->GetNumFibers());
         float currentOp = 0;
         fiberBundles.at(i)->GetFloatProperty("opacity", currentOp);
 
         if (currentOp!=op)
         {
           fib->SetFiberColors(255, 255, 255);
           fiberBundles.at(i)->SetFloatProperty("opacity", op);
           fiberBundles.at(i)->SetBoolProperty("Fiber2DfadeEFX", false);
         }
         m_InteractiveNode->SetData(extFB);
       }
       else
       {
         if (extFB->GetNumFibers()<=0)
         {
           QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
           continue;
         }
 
         mitk::DataNode::Pointer node;
         node = mitk::DataNode::New();
         node->SetData(extFB);
         QString name(fiberBundles.at(i)->GetName().c_str());
         name += "*";
         node->SetName(name.toStdString());
         node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(currentThickness));
         fiberBundles.at(i)->SetVisibility(false);
         GetDataStorage()->Add(node);
       }
     }
   }
   catch(const std::out_of_range& )
   {
     QMessageBox::warning( nullptr, "Fiber extraction failed", "Did you only create the planar figure, using the circle or polygon button, but forgot to actually place it in the image afterwards? \nAfter creating a planar figure, simply left-click at the desired position in the image or on the tractogram to place it.");
   }
 }
 
 void QmitkFiberProcessingView::GenerateAndComposite()
 {
   mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New();
   PFCAnd->setOperationType(mitk::PlanarFigureComposite::AND);
 
   mitk::DataNode::Pointer newPFCNode;
   newPFCNode = mitk::DataNode::New();
   newPFCNode->SetName("AND");
   newPFCNode->SetData(PFCAnd);
 
   AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
   RemoveObservers();
   m_SelectedPF.clear();
   m_SelectedPF.push_back(newPFCNode);
   AddObservers();
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::GenerateOrComposite()
 {
   mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New();
   PFCOr->setOperationType(mitk::PlanarFigureComposite::OR);
 
   mitk::DataNode::Pointer newPFCNode;
   newPFCNode = mitk::DataNode::New();
   newPFCNode->SetName("OR");
   newPFCNode->SetData(PFCOr);
 
   RemoveObservers();
   AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
   m_SelectedPF.clear();
   m_SelectedPF.push_back(newPFCNode);
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::GenerateNotComposite()
 {
   mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New();
   PFCNot->setOperationType(mitk::PlanarFigureComposite::NOT);
 
   mitk::DataNode::Pointer newPFCNode;
   newPFCNode = mitk::DataNode::New();
   newPFCNode->SetName("NOT");
   newPFCNode->SetData(PFCNot);
 
   RemoveObservers();
   AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
   m_SelectedPF.clear();
   m_SelectedPF.push_back(newPFCNode);
   AddObservers();
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::AddCompositeToDatastorage(mitk::DataNode::Pointer pfc, std::vector<mitk::DataNode::Pointer> children, mitk::DataNode::Pointer parentNode )
 {
   pfc->SetSelected(true);
   if (parentNode.IsNotNull())
     GetDataStorage()->Add(pfc, parentNode);
   else
     GetDataStorage()->Add(pfc);
 
   for (auto child : children)
   {
     if (dynamic_cast<PlanarFigure*>(child->GetData()))
     {
       mitk::DataNode::Pointer newChild;
       newChild = mitk::DataNode::New();
       newChild->SetData(dynamic_cast<PlanarFigure*>(child->GetData()));
       newChild->SetName( child->GetName() );
       newChild->SetBoolProperty("planarfigure.3drendering", true);
       newChild->SetBoolProperty("planarfigure.3drendering.fill", true);
 
       GetDataStorage()->Add(newChild, pfc);
       GetDataStorage()->Remove(child);
     }
     else if (dynamic_cast<PlanarFigureComposite*>(child->GetData()))
     {
       mitk::DataNode::Pointer newChild;
       newChild = mitk::DataNode::New();
       newChild->SetData(dynamic_cast<PlanarFigureComposite*>(child->GetData()));
       newChild->SetName( child->GetName() );
 
       std::vector< mitk::DataNode::Pointer > grandChildVector;
       mitk::DataStorage::SetOfObjects::ConstPointer grandchildren = GetDataStorage()->GetDerivations(child);
       for( mitk::DataStorage::SetOfObjects::const_iterator it = grandchildren->begin(); it != grandchildren->end(); ++it )
         grandChildVector.push_back(*it);
 
       AddCompositeToDatastorage(newChild, grandChildVector, pfc);
       GetDataStorage()->Remove(child);
     }
   }
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::CopyBundles()
 {
   if ( m_SelectedFB.empty() ){
     QMessageBox::information( nullptr, "Warning", "Select at least one fiber bundle!");
     MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!";
     return;
   }
 
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     mitk::FiberBundle::Pointer newFib = fib->GetDeepCopy();
 
     node->SetVisibility(false);
     QString name("");
     name += QString(m_SelectedFB.at(0)->GetName().c_str());
     name += "_copy";
 
     mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
     fbNode->SetData(newFib);
     fbNode->SetName(name.toStdString());
     fbNode->SetVisibility(true);
     GetDataStorage()->Add(fbNode);
   }
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::JoinBundles()
 {
   if ( m_SelectedFB.size()<2 ){
     QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!");
     MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!";
     return;
   }
 
   m_SelectedFB.at(0)->SetVisibility(false);
   mitk::FiberBundle::Pointer newBundle = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
 
   std::vector< mitk::FiberBundle::Pointer > tractograms;
   for (unsigned int i=1; i<m_SelectedFB.size(); i++)
   {
     m_SelectedFB.at(i)->SetVisibility(false);
     tractograms.push_back(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(i)->GetData()));
   }
   newBundle = newBundle->AddBundles(tractograms);
 
   mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
   fbNode->SetData(newBundle);
   fbNode->SetName("Joined_Tractograms");
   fbNode->SetVisibility(true);
   GetDataStorage()->Add(fbNode);
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::SubtractBundles()
 {
   if ( m_SelectedFB.size()<2 ){
     QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!");
     MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!";
     return;
   }
 
   mitk::FiberBundle::Pointer newBundle = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
   m_SelectedFB.at(0)->SetVisibility(false);
   QString name("");
   name += QString(m_SelectedFB.at(0)->GetName().c_str());
   for (unsigned int i=1; i<m_SelectedFB.size(); i++)
   {
     newBundle = newBundle->SubtractBundle(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(i)->GetData()));
     if (newBundle.IsNull())
       break;
     name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str());
     m_SelectedFB.at(i)->SetVisibility(false);
   }
   if (newBundle.IsNull())
   {
     QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!");
     return;
   }
 
   mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
   fbNode->SetData(newBundle);
   fbNode->SetName(name.toStdString());
   fbNode->SetVisibility(true);
   GetDataStorage()->Add(fbNode);
   UpdateGui();
 }
 
 void QmitkFiberProcessingView::ResampleSelectedBundlesSpline()
 {
   double factor = this->m_Controls->m_SmoothFibersBox->value();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     fib->ResampleSpline(factor);
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::ResampleSelectedBundlesLinear()
 {
   double factor = this->m_Controls->m_SmoothFibersBox->value();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     fib->ResampleLinear(factor);
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::CompressSelectedBundles()
 {
   double factor = this->m_Controls->m_ErrorThresholdBox->value();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     fib->Compress(factor);
     fib->ColorFibersByOrientation();
   }
   RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
 void QmitkFiberProcessingView::DoImageColorCoding()
 {
   if (m_Controls->m_ColorMapBox->GetSelectedNode().IsNull())
   {
     QMessageBox::information(nullptr, "Bundle coloring aborted:", "No image providing the scalar values for coloring the selected bundle available.");
     return;
   }
 
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     switch(m_Controls->m_LookupTableTypeBox->currentIndex())
     {
     case 0:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET, m_Controls->m_PercentileBox->value());
       break;
     case 1:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::HOT_IRON);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::HOT_IRON, m_Controls->m_PercentileBox->value());
       break;
     case 2:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::PLASMA);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::PLASMA, m_Controls->m_PercentileBox->value());
       break;
     case 3:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::INFERNO);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::INFERNO, m_Controls->m_PercentileBox->value());
       break;
     case 4:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::VIRIDIS);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::VIRIDIS, m_Controls->m_PercentileBox->value());
       break;
     case 5:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MAGMA);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MAGMA, m_Controls->m_PercentileBox->value());
       break;
     case 6:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::GRAYSCALE);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::GRAYSCALE, m_Controls->m_PercentileBox->value());
       break;
     case 7:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MULTILABEL);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MULTILABEL, 1.0);
       break;
     default:
-      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
+      fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET, m_Controls->m_PercentileBox->value());
     }
 
   }
 
   if (auto renderWindowPart = this->GetRenderWindowPart())
   {
     renderWindowPart->RequestUpdate();
   }
 }
 
 
 void QmitkFiberProcessingView::DoCurvatureColorCoding()
 {
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     switch(m_Controls->m_LookupTableTypeBox->currentIndex())
     {
     case 0:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
       break;
     case 1:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::HOT_IRON);
       break;
     case 2:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::PLASMA);
       break;
     case 3:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::INFERNO);
       break;
     case 4:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::VIRIDIS);
       break;
     case 5:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MAGMA);
       break;
     case 6:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::GRAYSCALE);
       break;
     case 7:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MULTILABEL);
       break;
     default:
       fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
     }
   }
 
   if (auto renderWindowPart = this->GetRenderWindowPart())
   {
     renderWindowPart->RequestUpdate();
   }
 }
 
 void QmitkFiberProcessingView::DoLengthColorCoding()
 {
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     switch(m_Controls->m_LookupTableTypeBox->currentIndex())
     {
     case 0:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
       break;
     case 1:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::HOT_IRON);
       break;
     case 2:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::PLASMA);
       break;
     case 3:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::INFERNO);
       break;
     case 4:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::VIRIDIS);
       break;
     case 5:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MAGMA);
       break;
     case 6:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::GRAYSCALE);
       break;
     case 7:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::MULTILABEL);
       break;
     default:
       fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_ValueAsWeightBox->isChecked(), mitk::LookupTable::JET);
     }
   }
 
   if (auto renderWindowPart = this->GetRenderWindowPart())
   {
     renderWindowPart->RequestUpdate();
   }
 }
 
 void QmitkFiberProcessingView::DoWeightColorCoding()
 {
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
     switch(m_Controls->m_LookupTableTypeBox->currentIndex())
     {
     case 0:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::JET);
       break;
     case 1:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::HOT_IRON);
       break;
     case 2:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::PLASMA);
       break;
     case 3:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::INFERNO);
       break;
     case 4:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::VIRIDIS);
       break;
     case 5:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::MAGMA);
       break;
     case 6:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::GRAYSCALE);
       break;
     case 7:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::MULTILABEL);
       break;
     default:
       fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), mitk::LookupTable::JET);
     }
   }
 
   if (auto renderWindowPart = this->GetRenderWindowPart())
   {
     renderWindowPart->RequestUpdate();
   }
 }
 
 void QmitkFiberProcessingView::MirrorFibers()
 {
   unsigned int axis = this->m_Controls->m_MirrorFibersBox->currentIndex();
   for (auto node : m_SelectedFB)
   {
     mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
     fib->MirrorFibers(axis);
   }
 
   for (auto surf : m_SelectedSurfaces)
   {
     vtkSmartPointer<vtkPolyData> poly = surf->GetVtkPolyData();
     vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
 
     for (int i=0; i<poly->GetNumberOfPoints(); i++)
     {
       double* point = poly->GetPoint(i);
       point[axis] *= -1;
       vtkNewPoints->InsertNextPoint(point);
     }
     poly->SetPoints(vtkNewPoints);
     surf->CalculateBoundingBox();
   }
 
   if (auto renderWindowPart = this->GetRenderWindowPart())
   {
     renderWindowPart->RequestUpdate();
   }
 }
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
index 749092b..3ca1430 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
@@ -1,1775 +1,1825 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <ui version="4.0">
  <class>QmitkFiberProcessingViewControls</class>
  <widget class="QWidget" name="QmitkFiberProcessingViewControls">
   <property name="geometry">
    <rect>
     <x>0</x>
     <y>0</y>
     <width>385</width>
     <height>711</height>
    </rect>
   </property>
   <property name="windowTitle">
    <string>Form</string>
   </property>
   <property name="styleSheet">
    <string>QCommandLinkButton:disabled {
   border: none;
 }
 
 QGroupBox {
   background-color: transparent;
 }</string>
   </property>
   <layout class="QGridLayout" name="gridLayout_3">
    <property name="leftMargin">
     <number>9</number>
    </property>
    <property name="topMargin">
     <number>9</number>
    </property>
    <property name="rightMargin">
     <number>9</number>
    </property>
    <property name="bottomMargin">
     <number>9</number>
    </property>
    <item row="1" column="0">
     <widget class="QToolBox" name="toolBoxx">
      <property name="font">
       <font>
        <weight>75</weight>
        <bold>true</bold>
       </font>
      </property>
      <property name="currentIndex">
-      <number>0</number>
+      <number>2</number>
      </property>
      <property name="tabSpacing">
       <number>5</number>
      </property>
      <widget class="QWidget" name="page">
       <property name="geometry">
        <rect>
         <x>0</x>
         <y>0</y>
         <width>353</width>
         <height>503</height>
        </rect>
       </property>
       <attribute name="label">
        <string>Fiber Extraction</string>
       </attribute>
       <attribute name="toolTip">
        <string>Extract a fiber subset from the selected fiber bundle using manually placed planar figures as waypoints or binary regions of interest.</string>
       </attribute>
       <layout class="QGridLayout" name="gridLayout_14">
        <item row="7" column="0">
         <spacer name="verticalSpacer_5">
          <property name="orientation">
           <enum>Qt::Vertical</enum>
          </property>
          <property name="sizeHint" stdset="0">
           <size>
            <width>20</width>
            <height>40</height>
           </size>
          </property>
         </spacer>
        </item>
        <item row="4" column="0">
         <widget class="QFrame" name="m_MaskExtractionFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_19">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <item row="2" column="0">
            <widget class="QLabel" name="m_FiberExtractionFractionLabel">
             <property name="text">
              <string>Min. overlap:</string>
             </property>
            </widget>
           </item>
           <item row="3" column="0">
            <widget class="QLabel" name="m_FiberExtractionThresholdLabel">
             <property name="text">
              <string>Threshold:</string>
             </property>
            </widget>
           </item>
           <item row="4" column="0">
            <widget class="QLabel" name="label_20">
             <property name="text">
              <string>Min. num. fibers:</string>
             </property>
            </widget>
           </item>
           <item row="3" column="2">
            <widget class="QDoubleSpinBox" name="m_FiberExtractionThresholdBox">
             <property name="toolTip">
              <string>Threshold on ROI image for positions to be considered as positive.</string>
             </property>
             <property name="decimals">
              <number>3</number>
             </property>
             <property name="maximum">
              <double>9999.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>0.500000000000000</double>
             </property>
            </widget>
           </item>
           <item row="0" column="2">
            <widget class="QComboBox" name="m_ExtractionBoxMask">
             <property name="sizePolicy">
              <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
               <horstretch>0</horstretch>
               <verstretch>0</verstretch>
              </sizepolicy>
             </property>
             <item>
              <property name="text">
               <string>Ending in ROI</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Not ending in ROI</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Passing ROI</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Not passing ROI</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Labelmap</string>
              </property>
             </item>
            </widget>
           </item>
           <item row="7" column="0">
            <widget class="QCheckBox" name="m_BothEnds">
             <property name="text">
              <string>Both ends</string>
             </property>
             <property name="checked">
              <bool>true</bool>
             </property>
            </widget>
           </item>
           <item row="6" column="0">
            <widget class="QCheckBox" name="m_InterpolateRoiBox">
             <property name="text">
              <string>Interpolate ROI </string>
             </property>
             <property name="checked">
              <bool>true</bool>
             </property>
            </widget>
           </item>
           <item row="4" column="2">
            <widget class="QSpinBox" name="m_MinExtractedFibersBox">
             <property name="minimum">
              <number>1</number>
             </property>
             <property name="maximum">
              <number>999999999</number>
             </property>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QLabel" name="label_16">
             <property name="text">
              <string>Extract fibers:</string>
             </property>
            </widget>
           </item>
           <item row="2" column="2">
            <widget class="QDoubleSpinBox" name="m_FiberExtractionFractionBox">
             <property name="toolTip">
              <string>Minimum overlap of streamlines and ROI in terms of streamline length. Zero means that one streamline point inside the ROI is enough to be considered as &quot;overlapping&quot;.</string>
             </property>
             <property name="decimals">
              <number>3</number>
             </property>
             <property name="maximum">
              <double>1.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
            </widget>
           </item>
           <item row="5" column="0">
            <widget class="QLabel" name="m_LabelsLabel">
             <property name="text">
              <string>Labels:</string>
             </property>
            </widget>
           </item>
           <item row="5" column="2">
            <widget class="QLineEdit" name="m_LabelsBox">
             <property name="toolTip">
              <string>Label values seperated by whitespace.</string>
             </property>
             <property name="text">
              <string>ALL</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="6" column="0">
         <widget class="QCommandLinkButton" name="m_ExtractFibersButton">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string>Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute.</string>
          </property>
          <property name="text">
           <string>Extract</string>
          </property>
         </widget>
        </item>
        <item row="0" column="0">
         <widget class="QComboBox" name="m_ExtractionMethodBox">
          <property name="sizePolicy">
           <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <item>
           <property name="text">
            <string>Extract using planar figures</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Extract using ROI image</string>
           </property>
          </item>
         </widget>
        </item>
        <item row="3" column="0">
         <widget class="QFrame" name="m_ExtactionFramePF">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_8">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="spacing">
            <number>6</number>
           </property>
           <item row="3" column="0">
            <widget class="QCheckBox" name="m_InteractiveBox">
             <property name="text">
              <string>Interactive Extraction</string>
             </property>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QFrame" name="m_PlanarFigureButtonsFrame">
             <property name="sizePolicy">
              <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
               <horstretch>0</horstretch>
               <verstretch>0</verstretch>
              </sizepolicy>
             </property>
             <property name="minimumSize">
              <size>
               <width>200</width>
               <height>0</height>
              </size>
             </property>
             <property name="maximumSize">
              <size>
               <width>16777215</width>
               <height>60</height>
              </size>
             </property>
             <property name="frameShape">
              <enum>QFrame::NoFrame</enum>
             </property>
             <property name="frameShadow">
              <enum>QFrame::Raised</enum>
             </property>
             <layout class="QGridLayout" name="gridLayout">
              <property name="leftMargin">
               <number>0</number>
              </property>
              <property name="topMargin">
               <number>0</number>
              </property>
              <property name="rightMargin">
               <number>0</number>
              </property>
              <property name="bottomMargin">
               <number>0</number>
              </property>
              <item row="0" column="0">
               <widget class="QPushButton" name="m_CircleButton">
                <property name="maximumSize">
                 <size>
                  <width>30</width>
                  <height>30</height>
                 </size>
                </property>
                <property name="toolTip">
                 <string>Draw circular ROI. Select reference fiber bundle to execute.</string>
                </property>
                <property name="text">
                 <string/>
                </property>
                <property name="icon">
                 <iconset resource="../../../../../release/MITK-build/private_plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc">
                  <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png</iconset>
                </property>
                <property name="iconSize">
                 <size>
                  <width>32</width>
                  <height>32</height>
                 </size>
                </property>
                <property name="checkable">
                 <bool>false</bool>
                </property>
                <property name="flat">
                 <bool>true</bool>
                </property>
               </widget>
              </item>
              <item row="0" column="2">
               <spacer name="horizontalSpacer">
                <property name="orientation">
                 <enum>Qt::Horizontal</enum>
                </property>
                <property name="sizeHint" stdset="0">
                 <size>
                  <width>40</width>
                  <height>20</height>
                 </size>
                </property>
               </spacer>
              </item>
              <item row="0" column="1">
               <widget class="QPushButton" name="m_PolygonButton">
                <property name="maximumSize">
                 <size>
                  <width>30</width>
                  <height>30</height>
                 </size>
                </property>
                <property name="toolTip">
                 <string>Draw polygonal ROI. Select reference fiber bundle to execute.</string>
                </property>
                <property name="text">
                 <string/>
                </property>
                <property name="icon">
                 <iconset resource="../../../../../release/MITK-build/private_plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc">
                  <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png</iconset>
                </property>
                <property name="iconSize">
                 <size>
                  <width>32</width>
                  <height>32</height>
                 </size>
                </property>
                <property name="checkable">
                 <bool>true</bool>
                </property>
                <property name="flat">
                 <bool>true</bool>
                </property>
               </widget>
              </item>
             </layout>
            </widget>
           </item>
           <item row="1" column="0">
            <widget class="QFrame" name="m_PlanarFigureButtonsFrame_2">
             <property name="sizePolicy">
              <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
               <horstretch>0</horstretch>
               <verstretch>0</verstretch>
              </sizepolicy>
             </property>
             <property name="minimumSize">
              <size>
               <width>200</width>
               <height>0</height>
              </size>
             </property>
             <property name="maximumSize">
              <size>
               <width>16777215</width>
               <height>60</height>
              </size>
             </property>
             <property name="frameShape">
              <enum>QFrame::NoFrame</enum>
             </property>
             <property name="frameShadow">
              <enum>QFrame::Raised</enum>
             </property>
             <layout class="QGridLayout" name="gridLayout_5">
              <property name="leftMargin">
               <number>0</number>
              </property>
              <property name="topMargin">
               <number>0</number>
              </property>
              <property name="rightMargin">
               <number>0</number>
              </property>
              <property name="bottomMargin">
               <number>0</number>
              </property>
              <item row="0" column="2">
               <widget class="QCommandLinkButton" name="PFCompoNOTButton">
                <property name="enabled">
                 <bool>false</bool>
                </property>
                <property name="maximumSize">
                 <size>
                  <width>60</width>
                  <height>16777215</height>
                 </size>
                </property>
                <property name="toolTip">
                 <string>Create NOT composition from selected ROI.</string>
                </property>
                <property name="text">
                 <string>NOT</string>
                </property>
               </widget>
              </item>
              <item row="0" column="1">
               <widget class="QCommandLinkButton" name="PFCompoORButton">
                <property name="enabled">
                 <bool>false</bool>
                </property>
                <property name="maximumSize">
                 <size>
                  <width>60</width>
                  <height>16777215</height>
                 </size>
                </property>
                <property name="toolTip">
                 <string>Create OR composition with selected ROIs.</string>
                </property>
                <property name="text">
                 <string>OR</string>
                </property>
               </widget>
              </item>
              <item row="0" column="3">
               <spacer name="horizontalSpacer_3">
                <property name="orientation">
                 <enum>Qt::Horizontal</enum>
                </property>
                <property name="sizeHint" stdset="0">
                 <size>
                  <width>40</width>
                  <height>20</height>
                 </size>
                </property>
               </spacer>
              </item>
              <item row="0" column="0">
               <widget class="QCommandLinkButton" name="PFCompoANDButton">
                <property name="enabled">
                 <bool>false</bool>
                </property>
                <property name="maximumSize">
                 <size>
                  <width>60</width>
                  <height>16777215</height>
                 </size>
                </property>
                <property name="toolTip">
                 <string>Create AND composition with selected ROIs.</string>
                </property>
                <property name="text">
                 <string>AND</string>
                </property>
               </widget>
              </item>
             </layout>
            </widget>
           </item>
           <item row="2" column="0">
            <widget class="QCommandLinkButton" name="m_GenerateRoiImage">
             <property name="enabled">
              <bool>false</bool>
             </property>
             <property name="sizePolicy">
              <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
               <horstretch>0</horstretch>
               <verstretch>0</verstretch>
              </sizepolicy>
             </property>
             <property name="maximumSize">
              <size>
               <width>16777215</width>
               <height>16777215</height>
              </size>
             </property>
             <property name="font">
              <font>
               <pointsize>11</pointsize>
              </font>
             </property>
             <property name="toolTip">
              <string>Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image.</string>
             </property>
             <property name="text">
              <string>Generate ROI Image</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="page_3">
       <property name="geometry">
        <rect>
         <x>0</x>
         <y>0</y>
         <width>353</width>
         <height>456</height>
        </rect>
       </property>
       <attribute name="label">
        <string>Fiber Removal</string>
       </attribute>
       <attribute name="toolTip">
        <string>Remove fibers that satisfy certain criteria from the selected bundle.</string>
       </attribute>
       <layout class="QGridLayout" name="gridLayout_4">
        <item row="1" column="0">
         <widget class="QFrame" name="m_RemoveDirectionFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_2">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <item row="0" column="0">
            <widget class="QLabel" name="label">
             <property name="text">
              <string>X:</string>
             </property>
            </widget>
           </item>
           <item row="1" column="0">
            <widget class="QLabel" name="label_3">
             <property name="text">
              <string>Y:</string>
             </property>
            </widget>
           </item>
           <item row="0" column="1">
            <widget class="QDoubleSpinBox" name="m_ExtractDirX"/>
           </item>
           <item row="1" column="1">
            <widget class="QDoubleSpinBox" name="m_ExtractDirY"/>
           </item>
           <item row="2" column="0">
            <widget class="QLabel" name="label_4">
             <property name="text">
              <string>Z:</string>
             </property>
            </widget>
           </item>
           <item row="2" column="1">
            <widget class="QDoubleSpinBox" name="m_ExtractDirZ"/>
           </item>
           <item row="3" column="0">
            <widget class="QLabel" name="label_5">
             <property name="text">
              <string>Angle:</string>
             </property>
            </widget>
           </item>
           <item row="3" column="1">
            <widget class="QDoubleSpinBox" name="m_ExtractAngle">
             <property name="toolTip">
              <string>Angular deviation threshold in degree</string>
             </property>
             <property name="decimals">
              <number>1</number>
             </property>
             <property name="maximum">
              <double>90.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>1.000000000000000</double>
             </property>
             <property name="value">
              <double>25.000000000000000</double>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="4" column="0">
         <widget class="QFrame" name="m_RemoveByWeightFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_20">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="spacing">
            <number>0</number>
           </property>
           <item row="1" column="0">
            <widget class="QLabel" name="label_18">
             <property name="text">
              <string>Weight threshold:</string>
             </property>
            </widget>
           </item>
           <item row="1" column="1">
            <widget class="QDoubleSpinBox" name="m_WeightThresholdBox">
             <property name="toolTip">
              <string>Only fibers with weight larger than this threshold are kept.</string>
             </property>
             <property name="decimals">
              <number>5</number>
             </property>
             <property name="maximum">
              <double>99999.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="6" column="0">
         <widget class="QCommandLinkButton" name="m_RemoveButton">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string/>
          </property>
          <property name="text">
           <string>Remove</string>
          </property>
         </widget>
        </item>
        <item row="0" column="0">
         <widget class="QComboBox" name="m_RemovalMethodBox">
          <property name="sizePolicy">
           <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <item>
           <property name="text">
            <string>Remove fibers in direction</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fibers by length</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fibers by curvature</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fiber parts outside mask</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fiber parts inside mask</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fibers by weight</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Remove fibers by tract density</string>
           </property>
          </item>
         </widget>
        </item>
        <item row="3" column="0">
         <widget class="QFrame" name="m_RemoveCurvatureFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_11">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <item row="2" column="2">
            <widget class="QCheckBox" name="m_RemoveCurvedFibersBox">
             <property name="toolTip">
              <string>If unchecked, the fiber exceeding the threshold will be split in two instead of removed.</string>
             </property>
             <property name="text">
              <string>Remove Fiber</string>
             </property>
             <property name="checked">
              <bool>false</bool>
             </property>
            </widget>
           </item>
           <item row="1" column="2">
            <widget class="QFrame" name="frame">
             <property name="frameShape">
              <enum>QFrame::NoFrame</enum>
             </property>
             <property name="frameShadow">
              <enum>QFrame::Raised</enum>
             </property>
             <layout class="QGridLayout" name="gridLayout_12">
              <property name="leftMargin">
               <number>0</number>
              </property>
              <property name="topMargin">
               <number>0</number>
              </property>
              <property name="rightMargin">
               <number>0</number>
              </property>
              <property name="bottomMargin">
               <number>0</number>
              </property>
              <property name="verticalSpacing">
               <number>0</number>
              </property>
              <item row="0" column="0">
               <widget class="QLabel" name="label_8">
                <property name="text">
                 <string>Max. Angular Deviation:</string>
                </property>
               </widget>
              </item>
              <item row="0" column="2">
               <spacer name="horizontalSpacer_5">
                <property name="orientation">
                 <enum>Qt::Horizontal</enum>
                </property>
                <property name="sizeHint" stdset="0">
                 <size>
                  <width>40</width>
                  <height>20</height>
                 </size>
                </property>
               </spacer>
              </item>
              <item row="0" column="1">
               <widget class="QDoubleSpinBox" name="m_CurvSpinBox">
                <property name="toolTip">
                 <string>Maximum angular deviation in degree</string>
                </property>
                <property name="maximum">
                 <double>180.000000000000000</double>
                </property>
                <property name="singleStep">
                 <double>0.100000000000000</double>
                </property>
                <property name="value">
                 <double>30.000000000000000</double>
                </property>
               </widget>
              </item>
              <item row="1" column="0">
               <widget class="QLabel" name="label_14">
                <property name="text">
                 <string>Distance:</string>
                </property>
               </widget>
              </item>
              <item row="1" column="1">
               <widget class="QDoubleSpinBox" name="m_CurvDistanceSpinBox">
                <property name="toolTip">
                 <string>Distance in mm</string>
                </property>
                <property name="decimals">
                 <number>1</number>
                </property>
                <property name="maximum">
                 <double>999.000000000000000</double>
                </property>
                <property name="singleStep">
                 <double>1.000000000000000</double>
                </property>
                <property name="value">
                 <double>10.000000000000000</double>
                </property>
               </widget>
              </item>
             </layout>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="7" column="0">
         <spacer name="verticalSpacer_4">
          <property name="orientation">
           <enum>Qt::Vertical</enum>
          </property>
          <property name="sizeHint" stdset="0">
           <size>
            <width>20</width>
            <height>40</height>
           </size>
          </property>
         </spacer>
        </item>
        <item row="2" column="0">
         <widget class="QFrame" name="m_RemoveLengthFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_6">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <item row="0" column="2">
            <spacer name="horizontalSpacer_4">
             <property name="orientation">
              <enum>Qt::Horizontal</enum>
             </property>
             <property name="sizeHint" stdset="0">
              <size>
               <width>40</width>
               <height>20</height>
              </size>
             </property>
            </spacer>
           </item>
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_PruneFibersMinBox">
             <property name="toolTip">
              <string>Minimum fiber length in mm</string>
             </property>
             <property name="minimum">
              <number>0</number>
             </property>
             <property name="maximum">
              <number>999999999</number>
             </property>
             <property name="value">
              <number>20</number>
             </property>
            </widget>
           </item>
           <item row="1" column="0">
            <widget class="QLabel" name="label_9">
             <property name="text">
              <string>Max. Length:</string>
             </property>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QLabel" name="label_7">
             <property name="text">
              <string>Min. Length:</string>
             </property>
            </widget>
           </item>
           <item row="1" column="1">
            <widget class="QSpinBox" name="m_PruneFibersMaxBox">
             <property name="toolTip">
              <string>Maximum fiber length in mm</string>
             </property>
             <property name="minimum">
              <number>0</number>
             </property>
             <property name="maximum">
              <number>999999999</number>
             </property>
             <property name="value">
              <number>300</number>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="5" column="0">
         <widget class="QFrame" name="m_RemoveByDensityFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_21">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <property name="verticalSpacing">
            <number>6</number>
           </property>
           <item row="1" column="1">
            <widget class="QDoubleSpinBox" name="m_DensityThresholdBox">
             <property name="toolTip">
              <string>Relative tract density (value between 0.0 and 1.0)</string>
             </property>
             <property name="decimals">
              <number>5</number>
             </property>
             <property name="minimum">
              <double>0.000000000000000</double>
             </property>
             <property name="maximum">
              <double>1.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>0.050000000000000</double>
             </property>
            </widget>
           </item>
           <item row="1" column="0">
            <widget class="QLabel" name="label_19">
             <property name="text">
              <string>Density threshold:</string>
             </property>
            </widget>
           </item>
           <item row="2" column="0">
            <widget class="QLabel" name="label_21">
             <property name="text">
              <string>Min. overlap:</string>
             </property>
            </widget>
           </item>
           <item row="2" column="1">
            <widget class="QDoubleSpinBox" name="m_DensityOverlapBox">
             <property name="toolTip">
              <string>Tracts have to spend at least this fraction of their length inside the specified density region.</string>
             </property>
             <property name="decimals">
              <number>3</number>
             </property>
             <property name="maximum">
              <double>1.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>0.500000000000000</double>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="page_4">
       <property name="geometry">
        <rect>
         <x>0</x>
         <y>0</y>
         <width>353</width>
-        <height>428</height>
+        <height>461</height>
        </rect>
       </property>
       <attribute name="label">
        <string>Bundle Modification</string>
       </attribute>
       <attribute name="toolTip">
        <string>Modify the selected bundle with operations such as fiber resampling, FA coloring, etc.</string>
       </attribute>
       <layout class="QGridLayout" name="gridLayout_10">
        <item row="2" column="0">
         <widget class="QFrame" name="m_CompressFibersFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_15">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <property name="verticalSpacing">
            <number>6</number>
           </property>
           <item row="0" column="0">
            <widget class="QLabel" name="label_10">
             <property name="text">
              <string>Error threshold in mm:</string>
             </property>
            </widget>
           </item>
           <item row="1" column="0">
            <widget class="QDoubleSpinBox" name="m_ErrorThresholdBox">
             <property name="maximum">
              <double>999999999.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>0.100000000000000</double>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="4" column="0">
         <widget class="QFrame" name="m_MirrorFibersFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_17">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <property name="verticalSpacing">
            <number>6</number>
           </property>
           <item row="1" column="0">
            <widget class="QComboBox" name="m_MirrorFibersBox">
             <item>
              <property name="text">
               <string>Sagittal</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Coronal</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>Axial</string>
              </property>
             </item>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QLabel" name="label_13">
             <property name="text">
              <string>Select direction:</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="3" column="0">
         <widget class="QFrame" name="m_ColorFibersFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_16">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <property name="verticalSpacing">
            <number>6</number>
           </property>
+          <item row="5" column="0">
+           <widget class="QmitkDataStorageComboBox" name="m_ColorMapBox"/>
+          </item>
           <item row="0" column="0">
            <widget class="QLabel" name="label_12">
             <property name="text">
              <string>Scalar map:</string>
             </property>
            </widget>
           </item>
-          <item row="4" column="0">
-           <widget class="QmitkDataStorageComboBox" name="m_ColorMapBox"/>
-          </item>
-          <item row="2" column="0">
-           <widget class="QCheckBox" name="m_ValueAsWeightBox">
-            <property name="toolTip">
-             <string>If checked, the (mean) unnormalized values per fiber are also used as fiber weights, e.g. the fiber length in mm.</string>
-            </property>
-            <property name="text">
-             <string>Values as weight</string>
-            </property>
-            <property name="checked">
-             <bool>false</bool>
-            </property>
-           </widget>
-          </item>
           <item row="1" column="0">
            <widget class="QCheckBox" name="m_FiberOpacityBox">
             <property name="toolTip">
              <string>If checked, the image values are not only used to color the fibers but are also used as opaxity values.</string>
             </property>
             <property name="text">
              <string>Values as opacity</string>
             </property>
             <property name="checked">
              <bool>false</bool>
             </property>
            </widget>
           </item>
-          <item row="3" column="0">
+          <item row="4" column="0">
            <widget class="QComboBox" name="m_LookupTableTypeBox">
             <item>
              <property name="text">
               <string>JET</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>HOT_IRON</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>PLASMA</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>INFERNO</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>VIRIDIS</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>MAGMA</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>GRAYSCALE</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>MULTILABEL</string>
              </property>
             </item>
            </widget>
           </item>
+          <item row="2" column="0">
+           <widget class="QCheckBox" name="m_ValueAsWeightBox">
+            <property name="toolTip">
+             <string>If checked, the (mean) unnormalized values per fiber are also used as fiber weights, e.g. the fiber length in mm.</string>
+            </property>
+            <property name="text">
+             <string>Values as weight</string>
+            </property>
+            <property name="checked">
+             <bool>false</bool>
+            </property>
+           </widget>
+          </item>
+          <item row="3" column="0">
+           <widget class="QFrame" name="frame_2">
+            <property name="frameShape">
+             <enum>QFrame::StyledPanel</enum>
+            </property>
+            <property name="frameShadow">
+             <enum>QFrame::Raised</enum>
+            </property>
+            <property name="lineWidth">
+             <number>0</number>
+            </property>
+            <layout class="QGridLayout" name="gridLayout_22">
+             <property name="leftMargin">
+              <number>0</number>
+             </property>
+             <property name="topMargin">
+              <number>0</number>
+             </property>
+             <property name="rightMargin">
+              <number>0</number>
+             </property>
+             <property name="bottomMargin">
+              <number>0</number>
+             </property>
+             <item row="0" column="0">
+              <widget class="QLabel" name="label_17">
+               <property name="text">
+                <string>Percentile:</string>
+               </property>
+              </widget>
+             </item>
+             <item row="0" column="1">
+              <widget class="QDoubleSpinBox" name="m_PercentileBox">
+               <property name="decimals">
+                <number>3</number>
+               </property>
+               <property name="maximum">
+                <double>1.000000000000000</double>
+               </property>
+               <property name="singleStep">
+                <double>0.100000000000000</double>
+               </property>
+               <property name="value">
+                <double>0.950000000000000</double>
+               </property>
+              </widget>
+             </item>
+            </layout>
+           </widget>
+          </item>
          </layout>
         </widget>
        </item>
        <item row="0" column="0">
         <widget class="QComboBox" name="m_ModificationMethodBox">
          <property name="sizePolicy">
           <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <item>
           <property name="text">
            <string>Resample fibers (spline)</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Resample fibers (linear)</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Compress fibers</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Mirror fibers</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Weight bundle</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color fibers by fiber weights</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by curvature</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by length</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by scalar map (e.g. FA)</string>
           </property>
          </item>
         </widget>
        </item>
        <item row="1" column="0">
         <widget class="QFrame" name="m_SmoothFibersFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_7">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="horizontalSpacing">
            <number>0</number>
           </property>
           <property name="verticalSpacing">
            <number>6</number>
           </property>
           <item row="1" column="0">
            <widget class="QDoubleSpinBox" name="m_SmoothFibersBox">
             <property name="minimum">
              <double>0.010000000000000</double>
             </property>
             <property name="maximum">
              <double>999999999.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>1.000000000000000</double>
             </property>
            </widget>
           </item>
           <item row="0" column="0">
            <widget class="QLabel" name="label_11">
             <property name="text">
              <string>Point distance in mm:</string>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
        <item row="7" column="0">
         <spacer name="verticalSpacer_3">
          <property name="orientation">
           <enum>Qt::Vertical</enum>
          </property>
          <property name="sizeHint" stdset="0">
           <size>
            <width>20</width>
            <height>40</height>
           </size>
          </property>
         </spacer>
        </item>
        <item row="6" column="0">
         <widget class="QCommandLinkButton" name="m_ModifyButton">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string/>
          </property>
          <property name="text">
           <string>Execute</string>
          </property>
         </widget>
        </item>
        <item row="5" column="0">
         <widget class="QFrame" name="m_BundleWeightFrame">
          <property name="frameShape">
           <enum>QFrame::NoFrame</enum>
          </property>
          <property name="frameShadow">
           <enum>QFrame::Raised</enum>
          </property>
          <layout class="QGridLayout" name="gridLayout_18">
           <property name="leftMargin">
            <number>0</number>
           </property>
           <property name="topMargin">
            <number>0</number>
           </property>
           <property name="rightMargin">
            <number>0</number>
           </property>
           <property name="bottomMargin">
            <number>0</number>
           </property>
           <property name="spacing">
            <number>0</number>
           </property>
           <item row="0" column="0">
            <widget class="QLabel" name="label_15">
             <property name="text">
              <string>Weight:</string>
             </property>
            </widget>
           </item>
           <item row="0" column="1">
            <widget class="QDoubleSpinBox" name="m_BundleWeightBox">
             <property name="decimals">
              <number>7</number>
             </property>
             <property name="maximum">
              <double>999999999.000000000000000</double>
             </property>
             <property name="singleStep">
              <double>0.100000000000000</double>
             </property>
             <property name="value">
              <double>1.000000000000000</double>
             </property>
            </widget>
           </item>
          </layout>
         </widget>
        </item>
       </layout>
      </widget>
      <widget class="QWidget" name="page_2">
       <property name="geometry">
        <rect>
         <x>0</x>
         <y>0</y>
         <width>367</width>
         <height>182</height>
        </rect>
       </property>
       <attribute name="label">
        <string>Bundle Operations</string>
       </attribute>
       <attribute name="toolTip">
        <string>Join, subtract or copy bundles.</string>
       </attribute>
       <layout class="QGridLayout" name="gridLayout_13">
        <item row="0" column="0">
         <widget class="QCommandLinkButton" name="m_SubstractBundles">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string>Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute.</string>
          </property>
          <property name="text">
           <string>Substract</string>
          </property>
         </widget>
        </item>
        <item row="2" column="0">
         <spacer name="verticalSpacer_2">
          <property name="orientation">
           <enum>Qt::Vertical</enum>
          </property>
          <property name="sizeHint" stdset="0">
           <size>
            <width>20</width>
            <height>40</height>
           </size>
          </property>
         </spacer>
        </item>
        <item row="0" column="2">
         <widget class="QCommandLinkButton" name="m_JoinBundles">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string>Merge selected fiber bundles. Select at least two fiber bundles to execute.</string>
          </property>
          <property name="text">
           <string>Join</string>
          </property>
         </widget>
        </item>
        <item row="1" column="0">
         <widget class="QCommandLinkButton" name="m_CopyBundle">
          <property name="enabled">
           <bool>false</bool>
          </property>
          <property name="sizePolicy">
           <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
            <horstretch>0</horstretch>
            <verstretch>0</verstretch>
           </sizepolicy>
          </property>
          <property name="maximumSize">
           <size>
            <width>200</width>
            <height>16777215</height>
           </size>
          </property>
          <property name="font">
           <font>
            <pointsize>11</pointsize>
           </font>
          </property>
          <property name="toolTip">
           <string>Merge selected fiber bundles. Select at least two fiber bundles to execute.</string>
          </property>
          <property name="text">
           <string>Copy</string>
          </property>
         </widget>
        </item>
       </layout>
      </widget>
     </widget>
    </item>
    <item row="0" column="0">
     <widget class="QGroupBox" name="m_InputData">
      <property name="title">
       <string>Please Select Input Data</string>
      </property>
      <layout class="QGridLayout" name="gridLayout_9">
       <property name="leftMargin">
        <number>6</number>
       </property>
       <property name="topMargin">
        <number>6</number>
       </property>
       <property name="rightMargin">
        <number>6</number>
       </property>
       <property name="bottomMargin">
        <number>6</number>
       </property>
       <item row="0" column="1">
        <widget class="QLabel" name="m_FibLabel">
         <property name="text">
          <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;&lt;span style=&quot; color:#ff0000;&quot;&gt;mandatory&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
         </property>
         <property name="wordWrap">
          <bool>true</bool>
         </property>
        </widget>
       </item>
       <item row="1" column="1">
        <widget class="QLabel" name="m_PfLabel">
         <property name="text">
          <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;&lt;span style=&quot; color:#969696;&quot;&gt;needed for extraction&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
         </property>
         <property name="wordWrap">
          <bool>true</bool>
         </property>
        </widget>
       </item>
       <item row="0" column="0">
        <widget class="QLabel" name="label_2">
         <property name="toolTip">
          <string>Input DTI</string>
         </property>
         <property name="text">
          <string>Fiber Bundle:</string>
         </property>
        </widget>
       </item>
       <item row="1" column="0">
        <widget class="QLabel" name="label_6">
         <property name="toolTip">
          <string>Binary seed ROI. If not specified, the whole image area is seeded.</string>
         </property>
         <property name="text">
          <string>ROI:</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </item>
    <item row="3" column="0">
     <spacer name="verticalSpacer">
      <property name="orientation">
       <enum>Qt::Vertical</enum>
      </property>
      <property name="sizeHint" stdset="0">
       <size>
        <width>20</width>
        <height>40</height>
       </size>
      </property>
     </spacer>
    </item>
   </layout>
  </widget>
  <customwidgets>
   <customwidget>
    <class>QmitkDataStorageComboBox</class>
    <extends>QComboBox</extends>
    <header location="global">QmitkDataStorageComboBox.h</header>
   </customwidget>
  </customwidgets>
  <resources>
   <include location="../../../../../release/MITK-build/private_plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc"/>
  </resources>
  <connections/>
 </ui>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp
index 92d2c93..cb09947 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp
@@ -1,656 +1,685 @@
 /*===================================================================
 
 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 <berryISelectionService.h>
 #include <berryIWorkbenchWindow.h>
 
 #include "QmitkTractometryView.h"
 
 #include <mitkNodePredicateDataType.h>
 #include <mitkNodePredicateDimension.h>
 #include <mitkNodePredicateAnd.h>
 #include <mitkImageCast.h>
 #include <mitkImageAccessByItk.h>
 #include <mitkImage.h>
 #include <mitkFiberBundle.h>
 #include <mitkDiffusionPropertyHelper.h>
 #include <mitkITKImageImport.h>
 #include <mitkPixelTypeMultiplex.h>
 #include <mitkImagePixelReadAccessor.h>
 #include <berryIPreferences.h>
 #include <berryWorkbenchPlugin.h>
 #include <berryQtPreferences.h>
 #include <vtkLookupTable.h>
 #include <QClipboard>
 #include <mitkLexicalCast.h>
 #include <QmitkChartWidget.h>
 #include <mitkLookupTable.h>
 #include <mitkTractClusteringFilter.h>
 #include <mitkClusteringMetricEuclideanStd.h>
 #include <itkTractDensityImageFilter.h>
 #include <itkTractParcellationFilter.h>
 #include <mitkLookupTableProperty.h>
 #include <mitkLevelWindowProperty.h>
+#include <itkMaskedStatisticsImageFilter.h>
 
 
 const std::string QmitkTractometryView::VIEW_ID = "org.mitk.views.tractometry";
 using namespace mitk;
 
 QmitkTractometryView::QmitkTractometryView()
   : QmitkAbstractView()
   , m_Controls( nullptr )
   , m_Visible(false)
 {
 
 }
 
 // Destructor
 QmitkTractometryView::~QmitkTractometryView()
 {
 
 }
 
 void QmitkTractometryView::CreateQtPartControl( QWidget *parent )
 {
   // build up qt view, unless already done
   if ( !m_Controls )
   {
     // create GUI widgets from the Qt Designer's .ui file
     m_Controls = new Ui::QmitkTractometryViewControls;
     m_Controls->setupUi( parent );
 
     connect( m_Controls->m_MethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) );
     connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartTractometry()) );
 
     mitk::TNodePredicateDataType<mitk::Image>::Pointer imageP = mitk::TNodePredicateDataType<mitk::Image>::New();
     mitk::NodePredicateDimension::Pointer dimP = mitk::NodePredicateDimension::New(3);
 
     m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
     m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP));
 
     m_Controls->m_ChartWidget->SetXAxisLabel("Tract position");
     m_Controls->m_ChartWidget->SetYAxisLabel("Image Value");
 
     m_Controls->m_ChartWidget->SetTheme(QmitkChartWidget::ColorTheme::darkstyle);
   }
 }
 
 void QmitkTractometryView::SetFocus()
 {
 }
 
 void QmitkTractometryView::UpdateGui()
 {
   berry::IWorkbenchPart::Pointer nullPart;
   OnSelectionChanged(nullPart, QList<mitk::DataNode::Pointer>(m_CurrentSelection));
 }
 
 bool QmitkTractometryView::Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer< vtkPolyData > ref_poly)
 {
   double d_direct = 0;
   double d_flipped = 0;
 
   vtkCell* cell1 = polydata1->GetCell(0);
   if (ref_poly!=nullptr)
     cell1 = ref_poly->GetCell(0);
   auto numPoints1 = cell1->GetNumberOfPoints();
   vtkPoints* points1 = cell1->GetPoints();
 
   std::vector<itk::Point<double, 3>> ref_points;
   for (int j=0; j<numPoints1; ++j)
   {
     double* p1 = points1->GetPoint(j);
     itk::Point<double, 3> itk_p;
     itk_p[0] = p1[0];
     itk_p[1] = p1[1];
     itk_p[2] = p1[2];
     ref_points.push_back(itk_p);
   }
 
   vtkCell* cell2 = polydata1->GetCell(i);
   vtkPoints* points2 = cell2->GetPoints();
 
   for (int j=0; j<numPoints1; ++j)
   {
     auto p1 = ref_points.at(j);
 
     double* p2 = points2->GetPoint(j);
     d_direct += (p1[0]-p2[0])*(p1[0]-p2[0]) + (p1[1]-p2[1])*(p1[1]-p2[1]) + (p1[2]-p2[2])*(p1[2]-p2[2]);
 
     double* p3 = points2->GetPoint(numPoints1-j-1);
     d_flipped += (p1[0]-p3[0])*(p1[0]-p3[0]) + (p1[1]-p3[1])*(p1[1]-p3[1]) + (p1[2]-p3[2])*(p1[2]-p3[2]);
   }
 
   if (d_direct>d_flipped)
     return true;
   return false;
 }
 
 template <typename TPixel>
 void QmitkTractometryView::StaticResamplingTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector<std::vector<double> > &data, std::string& clipboard_string)
 {
   mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
   unsigned int num_points = m_Controls->m_SamplingPointsBox->value();
   mitk::ImagePixelReadAccessor<TPixel,3> readimage(image, image->GetVolumeData(0));
   mitk::FiberBundle::Pointer working_fib = fib->GetDeepCopy();
   working_fib->ResampleToNumPoints(num_points);
   vtkSmartPointer< vtkPolyData > polydata = working_fib->GetFiberPolyData();
 
   double rgb[3] = {0,0,0};
 
   mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New();
   lookupTable->SetType(mitk::LookupTable::MULTILABEL);
 
   std::vector<std::vector<double> > all_values;
   std::vector< double > mean_values;
   for (unsigned int i=0; i<num_points; ++i)
     mean_values.push_back(0);
 
   double min = 100000.0;
   double max = 0;
   double mean = 0;
   for (unsigned int i=0; i<working_fib->GetNumFibers(); ++i)
   {
     vtkCell* cell = polydata->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     std::vector< double > fib_vals;
 
     bool flip = false;
     if (i>0)
       flip = Flip(polydata, i);
     else if (m_ReferencePolyData!=nullptr)
       flip = Flip(polydata, 0, m_ReferencePolyData);
 
     for (int j=0; j<numPoints; j++)
     {
       lookupTable->GetTableValue(j+1, rgb);
 
       double* p;
       if (flip)
       {
         auto p_idx = numPoints - j - 1;
         p = points->GetPoint(p_idx);
 
         working_fib->ColorSinglePoint(i, p_idx, rgb);
       }
       else
       {
         p = points->GetPoint(j);
 
         working_fib->ColorSinglePoint(i, j, rgb);
       }
 
       Point3D px;
       px[0] = p[0];
       px[1] = p[1];
       px[2] = p[2];
       double pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
       fib_vals.push_back(pixelValue);
       mean += pixelValue;
       if (pixelValue<min)
         min = pixelValue;
       else if (pixelValue>max)
         max = pixelValue;
 
       mean_values.at(j) += pixelValue;
 
     }
 
     all_values.push_back(fib_vals);
   }
 
   if (m_ReferencePolyData==nullptr)
     m_ReferencePolyData = polydata;
 
   std::vector< double > std_values1;
   std::vector< double > std_values2;
   for (unsigned int i=0; i<num_points; ++i)
   {
     mean_values.at(i) /= working_fib->GetNumFibers();
     double stdev = 0;
 
     for (unsigned int j=0; j<all_values.size(); ++j)
     {
       double diff = mean_values.at(i) - all_values.at(j).at(i);
       diff *= diff;
       stdev += diff;
     }
     stdev /= all_values.size();
     stdev = std::sqrt(stdev);
     std_values1.push_back(mean_values.at(i) + stdev);
     std_values2.push_back(mean_values.at(i) - stdev);
 
     clipboard_string += boost::lexical_cast<std::string>(mean_values.at(i));
     clipboard_string += " ";
     clipboard_string += boost::lexical_cast<std::string>(stdev);
     clipboard_string += "\n";
   }
   clipboard_string += "\n";
 
   data.push_back(mean_values);
   data.push_back(std_values1);
   data.push_back(std_values2);
 
   MITK_INFO << "Min: " << min;
   MITK_INFO << "Max: " << max;
   MITK_INFO << "Mean: " << mean/working_fib->GetNumberOfPoints();
 
   if (m_Controls->m_ShowBinned->isChecked())
   {
     mitk::DataNode::Pointer new_node = mitk::DataNode::New();
     auto children = GetDataStorage()->GetDerivations(node);
     for (unsigned int i=0; i<children->size(); ++i)
     {
       if (children->at(i)->GetName() == "binned_static")
       {
         new_node = children->at(i);
         new_node->SetData(working_fib);
         new_node->SetVisibility(true);
         node->SetVisibility(false);
         mitk::RenderingManager::GetInstance()->RequestUpdateAll();
         return;
       }
     }
 
     new_node->SetData(working_fib);
     new_node->SetName("binned_static");
     new_node->SetVisibility(true);
     node->SetVisibility(false);
     GetDataStorage()->Add(new_node, node);
   }
 }
 
 template <typename TPixel>
 void QmitkTractometryView::NearestCentroidPointTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string)
 {
   mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
   unsigned int num_points = m_Controls->m_SamplingPointsBox->value();
   mitk::ImagePixelReadAccessor<TPixel,3> readimage(image, image->GetVolumeData(0));
   mitk::FiberBundle::Pointer working_fib = fib->GetDeepCopy();
   working_fib->ResampleSpline(1.0);
   vtkSmartPointer< vtkPolyData > working_polydata = working_fib->GetFiberPolyData();
 
   // clustering
   std::vector< mitk::ClusteringMetric* > metrics;
   metrics.push_back({new mitk::ClusteringMetricEuclideanStd()});
 
   mitk::FiberBundle::Pointer fib_static_resampled = fib->GetDeepCopy();
   fib_static_resampled->ResampleToNumPoints(num_points);
   vtkSmartPointer< vtkPolyData > polydata_static_resampled = fib_static_resampled->GetFiberPolyData();
 
   std::vector<mitk::FiberBundle::Pointer> centroids;
   std::shared_ptr< mitk::TractClusteringFilter > clusterer = std::make_shared<mitk::TractClusteringFilter>();
   int c=0;
   while (c<30 && (centroids.empty() || centroids.size()>static_cast<unsigned long>(m_Controls->m_MaxCentroids->value())))
   {
     float cluster_size = m_Controls->m_ClusterSize->value() + m_Controls->m_ClusterSize->value()*c*0.2;
     float max_d = 0;
     int i=1;
     std::vector< float > distances;
     while (max_d < working_fib->GetGeometry()->GetDiagonalLength()/2)
     {
       distances.push_back(cluster_size*i);
       max_d = cluster_size*i;
       ++i;
     }
 
     clusterer->SetDistances(distances);
     clusterer->SetTractogram(fib_static_resampled);
     clusterer->SetMetrics(metrics);
     clusterer->SetMergeDuplicateThreshold(cluster_size);
     clusterer->SetDoResampling(false);
     clusterer->SetNumPoints(num_points);
   //  clusterer->SetMaxClusters(m_Controls->m_MaxCentroids->value());
     clusterer->SetMinClusterSize(1);
     clusterer->Update();
     centroids = clusterer->GetOutCentroids();
     ++c;
   }
 
   double rgb[3] = {0,0,0};
   mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New();
   lookupTable->SetType(mitk::LookupTable::MULTILABEL);
 
   std::vector<std::vector<double> > all_values;
   std::vector< double > mean_values;
   std::vector< unsigned int > value_count;
   for (unsigned int i=0; i<num_points; ++i)
   {
     mean_values.push_back(0);
     value_count.push_back(0);
   }
 
   double min = 100000.0;
   double max = 0;
   double mean = 0;
   for (unsigned int i=0; i<working_fib->GetNumFibers(); ++i)
   {
     vtkCell* cell = working_polydata->GetCell(i);
     auto numPoints = cell->GetNumberOfPoints();
     vtkPoints* points = cell->GetPoints();
 
     std::vector< double > fib_vals;
     for (int j=0; j<numPoints; j++)
     {
       double* p = points->GetPoint(j);
 
       int min_bin = 0;
       float d=999999;
       for (auto centroid : centroids)
       {
         auto centroid_polydata = centroid->GetFiberPolyData();
 
         vtkCell* centroid_cell = centroid_polydata->GetCell(0);
         auto centroid_numPoints = centroid_cell->GetNumberOfPoints();
         vtkPoints* centroid_points = centroid_cell->GetPoints();
 
         bool centroid_flip = Flip(centroid_polydata, 0, centroids.at(0)->GetFiberPolyData());
 
         for (int bin=0; bin<centroid_numPoints; ++bin)
         {
           double* centroid_p;
           centroid_p = centroid_points->GetPoint(bin);
           float temp_d = std::sqrt((p[0]-centroid_p[0])*(p[0]-centroid_p[0]) + (p[1]-centroid_p[1])*(p[1]-centroid_p[1]) + (p[2]-centroid_p[2])*(p[2]-centroid_p[2]));
           if (temp_d<d)
           {
             d = temp_d;
             if (centroid_flip)
               min_bin = centroid_numPoints-bin-1;
             else
               min_bin = bin;
           }
         }
 
       }
 
       lookupTable->GetTableValue(min_bin+1, rgb);
       working_fib->ColorSinglePoint(i, j, rgb);
 
       Point3D px;
       px[0] = p[0];
       px[1] = p[1];
       px[2] = p[2];
       double pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
       fib_vals.push_back(pixelValue);
       mean += pixelValue;
       if (pixelValue<min)
         min = pixelValue;
       else if (pixelValue>max)
         max = pixelValue;
 
       mean_values.at(min_bin) += pixelValue;
       value_count.at(min_bin) += 1;
     }
 
     all_values.push_back(fib_vals);
   }
 
   if (m_ReferencePolyData==nullptr)
     m_ReferencePolyData = working_polydata;
 
   std::vector< double > std_values1;
   std::vector< double > std_values2;
   for (unsigned int i=0; i<num_points; ++i)
   {
     mean_values.at(i) /= value_count.at(i);
     double stdev = 0;
 
     for (unsigned int j=0; j<all_values.size(); ++j)
     {
       double diff = mean_values.at(i) - all_values.at(j).at(i);
       diff *= diff;
       stdev += diff;
     }
     stdev /= all_values.size();
     stdev = std::sqrt(stdev);
     std_values1.push_back(mean_values.at(i) + stdev);
     std_values2.push_back(mean_values.at(i) - stdev);
 
     clipboard_string += boost::lexical_cast<std::string>(mean_values.at(i));
     clipboard_string += " ";
     clipboard_string += boost::lexical_cast<std::string>(stdev);
     clipboard_string += "\n";
   }
   clipboard_string += "\n";
 
   data.push_back(mean_values);
   data.push_back(std_values1);
   data.push_back(std_values2);
 
   MITK_INFO << "Min: " << min;
   MITK_INFO << "Max: " << max;
   MITK_INFO << "Mean: " << mean/working_fib->GetNumberOfPoints();
 
   if (m_Controls->m_ShowBinned->isChecked())
   {
     mitk::DataNode::Pointer new_node = mitk::DataNode::New();
 //    mitk::DataNode::Pointer new_node2;
     auto children = GetDataStorage()->GetDerivations(node);
     for (unsigned int i=0; i<children->size(); ++i)
     {
       if (children->at(i)->GetName() == "binned_centroid")
       {
         new_node = children->at(i);
         new_node->SetData(working_fib);
         new_node->SetVisibility(true);
         node->SetVisibility(false);
         mitk::RenderingManager::GetInstance()->RequestUpdateAll();
         return;
       }
     }
     new_node->SetData(working_fib);
     new_node->SetName("binned_centroid");
     new_node->SetVisibility(true);
     node->SetVisibility(false);
     GetDataStorage()->Add(new_node, node);
   }
 }
 
 void QmitkTractometryView::Activated()
 {
 
 }
 
 void QmitkTractometryView::Deactivated()
 {
 
 }
 
 void QmitkTractometryView::Visible()
 {
   m_Visible = true;
   QList<mitk::DataNode::Pointer> selection = GetDataManagerSelection();
   berry::IWorkbenchPart::Pointer nullPart;
   OnSelectionChanged(nullPart, selection);
 }
 
 void QmitkTractometryView::Hidden()
 {
   m_Visible = false;
 }
 
 std::string QmitkTractometryView::RGBToHexString(double *rgb)
 {
   std::ostringstream os;
   for (int i = 0; i < 3; ++i)
     {
     os << std::setw(2) << std::setfill('0') << std::hex
        << static_cast<int>(rgb[i] * 255);
     }
   return os.str();
 }
 
-void QmitkTractometryView::AlongTractRadiomicsPreprocessing(mitk::Image::Pointer image, mitk::DataNode::Pointer node)
+void QmitkTractometryView::AlongTractRadiomicsPreprocessing(mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string)
 {
   mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
 
   // calculate mask
-  typedef unsigned char OutPixType;
-  typedef itk::Image<OutPixType, 3> OutImageType;
-
-  OutImageType::Pointer itkImage = OutImageType::New();
+  typedef itk::Image<unsigned char, 3> ParcellationImageType;
+  ParcellationImageType::Pointer itkImage = ParcellationImageType::New();
   CastToItkImage(image, itkImage);
 
   itk::TractParcellationFilter< >::Pointer parcellator = itk::TractParcellationFilter< >::New();
   parcellator->SetInputImage(itkImage);
   parcellator->SetNumParcels(m_Controls->m_SamplingPointsBox->value());
   parcellator->SetInputTract(fib);
   parcellator->SetNumCentroids(m_Controls->m_MaxCentroids->value());
   parcellator->SetStartClusterSize(m_Controls->m_ClusterSize->value());
   parcellator->Update();
-  OutImageType::Pointer out_image = parcellator->GetOutput(0);
-  OutImageType::Pointer out_image_pp = parcellator->GetOutput(1);
+  ParcellationImageType::Pointer out_image = parcellator->GetOutput(0);
+  ParcellationImageType::Pointer out_image_pp = parcellator->GetOutput(1);
+  auto binary_masks = parcellator->GetBinarySplit(out_image_pp);
 
   mitk::Image::Pointer seg_img = mitk::Image::New();
   seg_img->InitializeByItk(out_image.GetPointer());
   seg_img->SetVolume(out_image->GetBufferPointer());
 
   mitk::Image::Pointer seg_img_pp = mitk::Image::New();
   seg_img_pp->InitializeByItk(out_image_pp.GetPointer());
   seg_img_pp->SetVolume(out_image_pp->GetBufferPointer());
 
+  std::vector< double > std_values1;
+  std::vector< double > std_values2;
+  std::vector< double > mean_values;
+  for (auto mask : binary_masks)
+  {
+    itk::Image<float, 3>::Pointer data_image = itk::Image<float, 3>::New();
+    CastToItkImage(image, data_image);
+    itk::MaskedStatisticsImageFilter<itk::Image<float, 3>>::Pointer statisticsImageFilter = itk::MaskedStatisticsImageFilter<itk::Image<float, 3>>::New();
+    statisticsImageFilter->SetInput(data_image);
+    statisticsImageFilter->SetMask(mask);
+    statisticsImageFilter->Update();
+    double mean = statisticsImageFilter->GetMean();
+    double stdev = std::sqrt(statisticsImageFilter->GetVariance());
+
+    std_values1.push_back(mean + stdev);
+    std_values2.push_back(mean - stdev);
+    mean_values.push_back(mean);
+
+    clipboard_string += boost::lexical_cast<std::string>(mean);
+    clipboard_string += " ";
+    clipboard_string += boost::lexical_cast<std::string>(stdev);
+    clipboard_string += "\n";
+  }
+  clipboard_string += "\n";
+
+  data.push_back(mean_values);
+  data.push_back(std_values1);
+  data.push_back(std_values2);
+
   mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
   lut->SetType( mitk::LookupTable::MULTILABEL );
   mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
   lut_prop->SetLookupTable( lut );
 
   mitk::LevelWindow lw;
   lw.SetRangeMinMax(0, parcellator->GetNumParcels());
 
-  mitk::DataNode::Pointer new_node = mitk::DataNode::New();
-  new_node->SetData(seg_img);
-  new_node->SetName("tract parcellation");
-  new_node->SetVisibility(true);
-  new_node->SetProperty("LookupTable", lut_prop );
-  new_node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
-  node->SetVisibility(false);
-  GetDataStorage()->Add(new_node, node);
+//  mitk::DataNode::Pointer new_node = mitk::DataNode::New();
+//  new_node->SetData(seg_img);
+//  new_node->SetName("tract parcellation");
+//  new_node->SetVisibility(true);
+//  new_node->SetProperty("LookupTable", lut_prop );
+//  new_node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
+//  node->SetVisibility(false);
+//  GetDataStorage()->Add(new_node, node);
 
   mitk::DataNode::Pointer new_node2 = mitk::DataNode::New();
   new_node2->SetData(seg_img_pp);
   new_node2->SetName("tract parcellation pp");
   new_node2->SetVisibility(false);
   new_node2->SetProperty("LookupTable", lut_prop );
   new_node2->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
-  GetDataStorage()->Add(new_node2, new_node);
+  GetDataStorage()->Add(new_node2, node);
 
   mitk::DataNode::Pointer new_node3 = mitk::DataNode::New();
-  auto working_fib = parcellator->GetWorkingTract();
-  working_fib->ColorFibersByScalarMap(seg_img, false, false, mitk::LookupTable::LookupTableType::MULTILABEL);
+  auto working_fib = fib->GetDeepCopy();
+  working_fib->ColorFibersByScalarMap(seg_img, false, false, mitk::LookupTable::LookupTableType::MULTILABEL, 0.9);
   new_node3->SetData(working_fib);
   new_node3->SetName("centroids");
-  GetDataStorage()->Add(new_node3, new_node);
+  GetDataStorage()->Add(new_node3, node);
 }
 
 void QmitkTractometryView::StartTractometry()
 {
   m_ReferencePolyData = nullptr;
 
   double color[3] = {0,0,0};
   mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New();
   lookupTable->SetType(mitk::LookupTable::MULTILABEL);
 
   mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData());
 
   this->m_Controls->m_ChartWidget->Clear();
   std::string clipboardString = "";
   int c = 1;
   for (auto node : m_CurrentSelection)
   {
     clipboardString += node->GetName() + "\n";
     clipboardString += "mean stdev\n";
 
     std::vector< std::vector< double > > data;
     switch (m_Controls->m_MethodBox->currentIndex())
     {
     case 0:
     {
       mitkPixelTypeMultiplex4( StaticResamplingTractometry, image->GetPixelType(), image, node, data, clipboardString );
       break;
     }
     case 1:
     {
       mitkPixelTypeMultiplex4( NearestCentroidPointTractometry, image->GetPixelType(), image, node, data, clipboardString );
       break;
     }
     case 2:
     {
-      AlongTractRadiomicsPreprocessing(image, node);
-      return;
+      AlongTractRadiomicsPreprocessing(image, node, data, clipboardString);
+      break;
     }
     default:
     {
       mitkPixelTypeMultiplex4( StaticResamplingTractometry, image->GetPixelType(), image, node, data, clipboardString );
     }
     }
 
     m_Controls->m_ChartWidget->AddData1D(data.at(0), node->GetName() + " Mean", QmitkChartWidget::ChartType::line);
     m_Controls->m_ChartWidget->SetLineStyle(node->GetName() + " Mean", QmitkChartWidget::LineStyle::solid);
     if (m_Controls->m_StDevBox->isChecked())
     {
       m_Controls->m_ChartWidget->AddData1D(data.at(1), node->GetName() + " +STDEV", QmitkChartWidget::ChartType::line);
       m_Controls->m_ChartWidget->AddData1D(data.at(2), node->GetName() + " -STDEV", QmitkChartWidget::ChartType::line);
       m_Controls->m_ChartWidget->SetLineStyle(node->GetName() + " +STDEV", QmitkChartWidget::LineStyle::dashed);
       m_Controls->m_ChartWidget->SetLineStyle(node->GetName() + " -STDEV", QmitkChartWidget::LineStyle::dashed);
     }
 
     lookupTable->GetTableValue(c, color);
     this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " Mean", RGBToHexString(color));
 
     if (m_Controls->m_StDevBox->isChecked())
     {
       color[0] *= 0.5;
       color[1] *= 0.5;
       color[2] *= 0.5;
       this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " +STDEV", RGBToHexString(color));
       this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " -STDEV", RGBToHexString(color));
     }
 
     this->m_Controls->m_ChartWidget->Show(true);
     this->m_Controls->m_ChartWidget->SetShowDataPoints(false);
     ++c;
   }
 
   QApplication::clipboard()->setText(clipboardString.c_str(), QClipboard::Clipboard);
 }
 
 void QmitkTractometryView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes)
 {
   m_Controls->m_StartButton->setEnabled(false);
 
   if (!m_Visible)
     return;
 
   if (m_Controls->m_MethodBox->currentIndex()==0)
     m_Controls->m_ClusterFrame->setVisible(false);
   else
     m_Controls->m_ClusterFrame->setVisible(true);
 
   m_CurrentSelection.clear();
   if(m_Controls->m_ImageBox->GetSelectedNode().IsNull())
     return;
 
   for (auto node: nodes)
     if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
       m_CurrentSelection.push_back(node);
   if (!m_CurrentSelection.empty())
     m_Controls->m_StartButton->setEnabled(true);
 }
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h
index e610038..1fd0365 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h
@@ -1,86 +1,86 @@
 /*===================================================================
 
 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.
 
 ===================================================================*/
 
 #ifndef QmitkTractometryView_h
 #define QmitkTractometryView_h
 
 #include <QmitkAbstractView.h>
 #include "ui_QmitkTractometryViewControls.h"
 #include <itkImage.h>
 #include <mitkImage.h>
 #include <mitkPixelType.h>
 #include <mitkFiberBundle.h>
 #include <mitkILifecycleAwarePart.h>
 #include <QmitkChartWidget.h>
 
 /*!
 \brief Weight fibers by linearly fitting them to the image data.
 
 */
 class QmitkTractometryView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
 {
   // this is needed for all Qt objects that should have a Qt meta-object
   // (everything that derives from QObject and wants to have signal/slots)
   Q_OBJECT
 
 public:
 
   static const std::string VIEW_ID;
 
   QmitkTractometryView();
   virtual ~QmitkTractometryView();
 
   virtual void CreateQtPartControl(QWidget *parent) override;
 
   template <typename TPixel>
   void StaticResamplingTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string);
 
   template <typename TPixel>
   void NearestCentroidPointTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string);
 
-  void AlongTractRadiomicsPreprocessing(mitk::Image::Pointer image, mitk::DataNode::Pointer node);
+  void AlongTractRadiomicsPreprocessing(mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector<std::vector<double> > &data, std::string &clipboard_string);
 
   virtual void SetFocus() override;
 
   virtual void Activated() override;
   virtual void Deactivated() override;
   virtual void Visible() override;
   virtual void Hidden() override;
 
 protected slots:
 
   void UpdateGui();
   void StartTractometry();
 
 protected:
 
   /// \brief called by QmitkAbstractView when DataManager's selection has changed
   virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
 
   Ui::QmitkTractometryViewControls* m_Controls;
 
   bool Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer<vtkPolyData> ref_poly=nullptr);
   std::string RGBToHexString(double *rgb);
 
   vtkSmartPointer< vtkPolyData > m_ReferencePolyData;
   QList<mitk::DataNode::Pointer> m_CurrentSelection;
   bool  m_Visible;
 };
 
 
 
 #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
 
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui
index cfdf1a0..aac3a4d 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui
@@ -1,235 +1,225 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <ui version="4.0">
  <class>QmitkTractometryViewControls</class>
  <widget class="QWidget" name="QmitkTractometryViewControls">
   <property name="geometry">
    <rect>
     <x>0</x>
     <y>0</y>
     <width>484</width>
     <height>951</height>
    </rect>
   </property>
   <property name="windowTitle">
    <string>Form</string>
   </property>
   <property name="styleSheet">
    <string>QCommandLinkButton:disabled {
   border: none;
 }
 
 QGroupBox {
   background-color: transparent;
 }</string>
   </property>
   <layout class="QGridLayout" name="gridLayout_10">
    <item row="6" column="0">
     <spacer name="verticalSpacer">
      <property name="orientation">
       <enum>Qt::Vertical</enum>
      </property>
      <property name="sizeHint" stdset="0">
       <size>
        <width>20</width>
        <height>40</height>
       </size>
      </property>
     </spacer>
    </item>
    <item row="3" column="0">
     <widget class="QCheckBox" name="m_StDevBox">
      <property name="text">
       <string>Show STDEV</string>
      </property>
      <property name="checked">
       <bool>true</bool>
      </property>
     </widget>
    </item>
    <item row="4" column="0">
     <widget class="QCheckBox" name="m_ShowBinned">
      <property name="text">
       <string>Show binned tract</string>
      </property>
      <property name="checked">
       <bool>true</bool>
      </property>
     </widget>
    </item>
    <item row="5" column="0">
     <widget class="QmitkChartWidget" name="m_ChartWidget" native="true">
      <property name="minimumSize">
       <size>
        <width>0</width>
        <height>600</height>
       </size>
      </property>
     </widget>
    </item>
    <item row="2" column="0">
     <widget class="QGroupBox" name="m_ClusterFrame">
      <property name="title">
       <string>Centroid Options</string>
      </property>
      <layout class="QGridLayout" name="gridLayout">
-      <item row="1" column="1">
-       <widget class="QDoubleSpinBox" name="m_ClusterSize">
+      <item row="0" column="1">
+       <widget class="QSpinBox" name="m_MaxCentroids">
+        <property name="minimum">
+         <number>0</number>
+        </property>
+        <property name="maximum">
+         <number>9999</number>
+        </property>
         <property name="value">
-         <double>15.000000000000000</double>
+         <number>0</number>
         </property>
        </widget>
       </item>
       <item row="1" column="0">
        <widget class="QLabel" name="label_6">
         <property name="text">
          <string>Cluster Size:</string>
         </property>
        </widget>
       </item>
       <item row="0" column="0">
        <widget class="QLabel" name="label_5">
         <property name="text">
          <string>Max. Number of Centroids:</string>
         </property>
        </widget>
       </item>
-      <item row="0" column="1">
-       <widget class="QSpinBox" name="m_MaxCentroids">
-        <property name="minimum">
-         <number>0</number>
-        </property>
-        <property name="maximum">
-         <number>9999</number>
-        </property>
+      <item row="1" column="1">
+       <widget class="QDoubleSpinBox" name="m_ClusterSize">
         <property name="value">
-         <number>0</number>
-        </property>
-       </widget>
-      </item>
-      <item row="2" column="0">
-       <widget class="QCheckBox" name="m_PostprocessParcellation">
-        <property name="text">
-         <string>Postprocess Parcellation</string>
-        </property>
-        <property name="checked">
-         <bool>true</bool>
+         <double>15.000000000000000</double>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </item>
    <item row="0" column="0">
     <widget class="QFrame" name="frame">
      <property name="frameShape">
       <enum>QFrame::NoFrame</enum>
      </property>
      <property name="frameShadow">
       <enum>QFrame::Raised</enum>
      </property>
      <layout class="QGridLayout" name="gridLayout_2">
       <property name="leftMargin">
        <number>0</number>
       </property>
       <property name="topMargin">
        <number>0</number>
       </property>
       <property name="rightMargin">
        <number>0</number>
       </property>
       <property name="bottomMargin">
        <number>0</number>
       </property>
       <property name="spacing">
        <number>6</number>
       </property>
       <item row="0" column="1">
        <widget class="QmitkDataStorageComboBox" name="m_ImageBox">
         <property name="toolTip">
          <string/>
         </property>
        </widget>
       </item>
       <item row="2" column="1">
        <widget class="QSpinBox" name="m_SamplingPointsBox">
         <property name="minimum">
          <number>0</number>
         </property>
         <property name="maximum">
          <number>99999</number>
         </property>
         <property name="value">
-         <number>15</number>
+         <number>0</number>
         </property>
        </widget>
       </item>
       <item row="0" column="0">
        <widget class="QLabel" name="label_3">
         <property name="text">
          <string>Input Image:</string>
         </property>
        </widget>
       </item>
       <item row="2" column="0">
        <widget class="QLabel" name="label_4">
         <property name="text">
          <string>Sampling Points:</string>
         </property>
        </widget>
       </item>
       <item row="1" column="1">
        <widget class="QComboBox" name="m_MethodBox">
         <property name="currentIndex">
          <number>2</number>
         </property>
         <item>
          <property name="text">
           <string>Static Resampling</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>Centroid Based</string>
          </property>
         </item>
         <item>
          <property name="text">
           <string>Segment voting</string>
          </property>
         </item>
        </widget>
       </item>
       <item row="1" column="0">
        <widget class="QLabel" name="label_7">
         <property name="text">
          <string>Binning Method:</string>
         </property>
        </widget>
       </item>
      </layout>
     </widget>
    </item>
    <item row="1" column="0">
     <widget class="QCommandLinkButton" name="m_StartButton">
      <property name="text">
       <string>Start Tractometry</string>
      </property>
     </widget>
    </item>
   </layout>
  </widget>
  <customwidgets>
   <customwidget>
    <class>QmitkDataStorageComboBox</class>
    <extends>QComboBox</extends>
    <header location="global">QmitkDataStorageComboBox.h</header>
   </customwidget>
   <customwidget>
    <class>QmitkChartWidget</class>
    <extends>QWidget</extends>
    <header location="global">QmitkChartWidget.h</header>
   </customwidget>
  </customwidgets>
  <resources/>
  <connections/>
 </ui>