diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
index 7aedb2bc5a..1f2272d85f 100644
--- a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
+++ b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
@@ -1,941 +1,964 @@
 /*=========================================================================
 
  Program:   Medical Imaging & Interaction Toolkit
  Language:  C++
  Date:      $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $
  Version:   $Revision: 21975 $
 
  Copyright (c) German Cancer Research Center, Division of Medical and
  Biological Informatics. All rights reserved.
  See MITKCopyright.txt or http://www.mitk.org/copyright.html for details.
 
  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.  See the above copyright notices for more information.
 
  =========================================================================*/
 
 
 #include "mitkFiberBundleX.h"
 
 #include <mitkPlanarCircle.h>
 #include <mitkPlanarPolygon.h>
 #include <mitkPlanarFigureComposite.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>
 
 const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient";
 const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "Color_FA";
 const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs";
 const char* mitk::FiberBundleX::FA_VALUE_ARRAY = "FA_Values";
 
 mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData )
     : m_currentColorCoding(NULL)
     , m_isModified(false)
     , m_NumFibers(0)
 {
     if (fiberPolyData == NULL)
         m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     else
         m_FiberPolyData = fiberPolyData;
 
     m_NumFibers = m_FiberPolyData->GetNumberOfLines();
 
     UpdateFiberGeometry();
 }
 
 mitk::FiberBundleX::~FiberBundleX()
 {
 
 }
 
 mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy()
 {
     mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New();
 
     //  newFib->m_FiberIdDataSet = vtkSmartPointer<vtkDataSet>::New();
     //  newFib->m_FiberIdDataSet->DeepCopy(m_FiberIdDataSet);
     newFib->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     newFib->m_FiberPolyData->DeepCopy(m_FiberPolyData);
     newFib->SetColorCoding(m_currentColorCoding);
     newFib->m_isModified = m_isModified;
     newFib->m_NumFibers = m_NumFibers;
     newFib->UpdateFiberGeometry();
 
     return newFib;
 }
 
 vtkSmartPointer<vtkPolyData> mitk::FiberBundleX::GenerateNewFiberBundleByIds(std::vector<unsigned long> fiberIds)
 {
+    MITK_INFO << "\n=====FINAL RESULT: fib_id ======\n";
+    MITK_INFO << "Number of new Fibers: " << fiberIds.size();
+    // iterate through the vectorcontainer hosting all desired fiber Ids
 
     vtkSmartPointer<vtkPolyData> newFiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     vtkSmartPointer<vtkCellArray> newLineSet = vtkSmartPointer<vtkCellArray>::New();
     vtkSmartPointer<vtkPoints> newPointSet = vtkSmartPointer<vtkPoints>::New();
 
-    MITK_INFO << "\n=====FINAL RESULT: fib_id ======\n";
-    MITK_INFO << "Number of new Fibers: " << fiberIds.size();
-    // iterate through the vectorcontainer hosting all desired fiber Ids
+    // if FA array available, initialize fa double array
+    // if color orient array is available init color array
+    vtkSmartPointer<vtkDoubleArray> faValueArray;
+    vtkSmartPointer<vtkUnsignedCharArray> colorsT;
+    //colors and alpha value for each single point, RGBA = 4 components
+    unsigned char rgba[4] = {0,0,0,0};
+    int componentSize = sizeof(rgba);
+
+    if (m_FiberIdDataSet->GetPointData()->HasArray(FA_VALUE_ARRAY)){
+        MITK_INFO << "FA VALUES AVAILABLE, init array for new fiberbundle";
+        faValueArray = vtkSmartPointer<vtkDoubleArray>::New();
+    }
+
+    if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){
+        MITK_INFO << "colorValues available, init array for new fiberbundle";
+        colorsT = vtkUnsignedCharArray::New();
+        colorsT->SetNumberOfComponents(componentSize);
+        colorsT->SetName(COLORCODING_ORIENTATION_BASED);
+    }
+
+
 
     std::vector<unsigned long>::iterator finIt = fiberIds.begin();
     while ( finIt != fiberIds.end() )
     {
 //        MITK_INFO << *finIt;
         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++)
         {
 //            MITK_INFO << "id: " << fiber->GetPointId(i);
 //            MITK_INFO << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2];
             newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints());
             newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]);
 
+
             if (m_FiberIdDataSet->GetPointData()->HasArray(FA_VALUE_ARRAY)){
-                MITK_INFO << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i));
+//                MITK_INFO << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i));
             }
 
             if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){
-                MITK_INFO << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i));
+//                MITK_INFO << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0];
             }
         }
 
         newLineSet->InsertNextCell(newFiber);
         ++finIt;
     }
 
     newFiberPolyData->SetPoints(newPointSet);
     newFiberPolyData->SetLines(newLineSet);
     MITK_INFO << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints();
     MITK_INFO << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines();
     MITK_INFO << "=====================\n";
 
 //    mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData);
     return newFiberPolyData;
 }
 
 // merge two fiber bundles
 mitk::FiberBundleX::Pointer mitk::FiberBundleX::operator+(mitk::FiberBundleX* fib)
 {
 
     vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
     vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
     vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
     vtkSmartPointer<vtkCellArray> vLines = m_FiberPolyData->GetLines();
     vLines->InitTraversal();
 
     // add current fiber bundle
     int numFibers = GetNumFibers();
     for( int i=0; i<numFibers; i++ )
     {
         vtkIdType   numPoints(0);
         vtkIdType*  points(NULL);
         vLines->GetNextCell ( numPoints, points );
 
         vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
         for( int j=0; j<numPoints; j++)
         {
             vtkIdType id = vNewPoints->InsertNextPoint(m_FiberPolyData->GetPoint(points[j]));
             container->GetPointIds()->InsertNextId(id);
         }
         vNewLines->InsertNextCell(container);
     }
 
     vLines = fib->m_FiberPolyData->GetLines();
     vLines->InitTraversal();
 
     // add new fiber bundle
     numFibers = fib->GetNumFibers();
     for( int i=0; i<numFibers; i++ )
     {
         vtkIdType   numPoints(0);
         vtkIdType*  points(NULL);
         vLines->GetNextCell ( numPoints, points );
 
         vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
         for( int j=0; j<numPoints; j++)
         {
             vtkIdType id = vNewPoints->InsertNextPoint(fib->m_FiberPolyData->GetPoint(points[j]));
             container->GetPointIds()->InsertNextId(id);
         }
         vNewLines->InsertNextCell(container);
     }
 
     // initialize polydata
     vNewPolyData->SetPoints(vNewPoints);
     vNewPolyData->SetLines(vNewLines);
 
     // initialize fiber bundle
     mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData);
     return newFib;
 }
 
 // subtract two fiber bundles
 mitk::FiberBundleX::Pointer mitk::FiberBundleX::operator-(mitk::FiberBundleX* fib)
 {
 
     vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
     vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
     vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
 
     vtkSmartPointer<vtkCellArray> vLines = m_FiberPolyData->GetLines();
     vLines->InitTraversal();
 
     // iterate over current fibers
     int numFibers = GetNumFibers();
     for( int i=0; i<numFibers; i++ )
     {
         vtkIdType   numPoints(0);
         vtkIdType*  points(NULL);
         vLines->GetNextCell ( numPoints, points );
 
         vtkSmartPointer<vtkCellArray> vLines2 = fib->m_FiberPolyData->GetLines();
         vLines2->InitTraversal();
         int numFibers2 = fib->GetNumFibers();
         bool contained = false;
         for( int i2=0; i2<numFibers2; i2++ )
         {
             vtkIdType   numPoints2(0);
             vtkIdType*  points2(NULL);
             vLines2->GetNextCell ( numPoints2, points2 );
 
             // check endpoints
             itk::Point<float, 3> point_start = GetItkPoint(m_FiberPolyData->GetPoint(points[0]));
             itk::Point<float, 3> point_end = GetItkPoint(m_FiberPolyData->GetPoint(points[numPoints-1]));
             itk::Point<float, 3> point2_start = GetItkPoint(fib->m_FiberPolyData->GetPoint(points2[0]));
             itk::Point<float, 3> point2_end = GetItkPoint(fib->m_FiberPolyData->GetPoint(points2[numPoints2-1]));
 
             if (point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps ||
                     point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)
             {
                 // further checking ???
                 contained = true;
             }
         }
 
         // add to result because fiber is not subtracted
         if (!contained)
         {
             vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
             for( int j=0; j<numPoints; j++)
             {
                 vtkIdType id = vNewPoints->InsertNextPoint(m_FiberPolyData->GetPoint(points[j]));
                 container->GetPointIds()->InsertNextId(id);
             }
             vNewLines->InsertNextCell(container);
         }
     }
 
     // initialize polydata
     vNewPolyData->SetPoints(vNewPoints);
     vNewPolyData->SetLines(vNewLines);
 
     // initialize fiber bundle
     mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData);
     return newFib;
 }
 
 itk::Point<float, 3> mitk::FiberBundleX::GetItkPoint(double point[3])
 {
     itk::Point<float, 3> itkPoint;
     itkPoint[0] = point[0];
     itkPoint[1] = point[1];
     itkPoint[2] = point[2];
     return itkPoint;
 }
 
 /*
  * set polydata (additional flag to recompute fiber geometry, default = true)
  */
 void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer<vtkPolyData> fiberPD, bool updateGeometry)
 {
     if (fiberPD == NULL)
         this->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
     else
         this->m_FiberPolyData = fiberPD;
 
     if (updateGeometry)
         UpdateFiberGeometry();
 
     m_NumFibers = m_FiberPolyData->GetNumberOfLines();
 
     m_isModified = true;
 }
 
 /*
  * return vtkPolyData
  */
 vtkSmartPointer<vtkPolyData> mitk::FiberBundleX::GetFiberPolyData()
 {
     return m_FiberPolyData;
 }
 
 void mitk::FiberBundleX::DoColorCodingOrientationbased()
 {
     //===== 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
     //=================================================
 
 
     /*  make sure that processing colorcoding is only called when necessary */
     if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) &&
          m_FiberPolyData->GetNumberOfPoints() ==
          m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() )
     {
         // fiberstructure is already colorcoded
         MITK_INFO << " NO NEED TO REGENERATE COLORCODING! " ;
         return;
     }
 
     /* Finally, execute color calculation */
     vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
     int numOfPoints = extrPoints->GetNumberOfPoints();
 
     //colors and alpha value for each single point, RGBA = 4 components
     unsigned char rgba[4] = {0,0,0,0};
     int componentSize = sizeof(rgba);
 
     vtkSmartPointer<vtkUnsignedCharArray> colorsT = vtkUnsignedCharArray::New();
     colorsT->Allocate(numOfPoints * componentSize);
     colorsT->SetNumberOfComponents(componentSize);
     colorsT->SetName(COLORCODING_ORIENTATION_BASED);
 
 
 
     /* checkpoint: does polydata contain any fibers */
     int numOfFibers = m_FiberPolyData->GetNumberOfLines();
     if (numOfFibers < 1) {
         MITK_INFO << "\n ========= Number of Fibers is 0 and below ========= \n";
         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 pointsPerFiber; // number of points for current line
         fiberList->GetNextCell(pointsPerFiber, idList);
 
         //    MITK_INFO << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ;
 
         /* 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 except 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] = (unsigned char) (255.0 * std::fabs(diff[0]));
                     rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1]));
                     rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2]));
                     rgba[3] = (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] = (unsigned char) (255.0 * std::fabs(diff1[0]));
                     rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1]));
                     rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2]));
                     rgba[3] = (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] = (unsigned char) (255.0 * std::fabs(diff2[0]));
                     rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1]));
                     rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2]));
                     rgba[3] = (unsigned char) (255.0);
 
                 }
 
                 colorsT->InsertTupleValue(idList[i], rgba);
 
             } //end for loop
 
         } else if (pointsPerFiber == 1) {
             /* a single point does not define a fiber (use vertex mechanisms instead */
             continue;
             //      colorsT->InsertTupleValue(0, rgba);
 
         } else {
             MITK_INFO << "Fiber with 0 points detected... please check your tractography algorithm!" ;
             continue;
 
         }
 
 
     }//end for loop
 
     m_FiberPolyData->GetPointData()->AddArray(colorsT);
 
     /*=========================
       - this is more relevant for renderer than for fiberbundleX datastructure
       - think about sourcing this to a explicit method which coordinates colorcoding */
     this->SetColorCoding(COLORCODING_ORIENTATION_BASED);
     m_isModified = true;
     //  ===========================
 
     //mini test, shall be ported to MITK TESTINGS!
     if (colorsT->GetSize() != numOfPoints*componentSize) {
         MITK_INFO << "ALLOCATION ERROR IN INITIATING COLOR ARRAY";
     }
 
 }
 
 void mitk::FiberBundleX::DoGenerateFiberIds()
 {
     if (m_FiberPolyData == NULL)
         return;
 
     //  for (int i=0; i<10000000; ++i)
     //  {
     //   if(i%500 == 0)
     //     MITK_INFO << i;
     //  }
     //  MITK_INFO << "Generating Fiber Ids";
     vtkSmartPointer<vtkIdFilter> idFiberFilter = vtkSmartPointer<vtkIdFilter>::New();
     idFiberFilter->SetInput(m_FiberPolyData);
     idFiberFilter->CellIdsOn();
     //  idFiberFilter->PointIdsOn(); // point id's are not needed
     idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY);
     idFiberFilter->FieldDataOn();
     idFiberFilter->Update();
 
     m_FiberIdDataSet = idFiberFilter->GetOutput();
 
     MITK_INFO << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells();
 
 }
 
 
 //temporarely include only
 //#include <vtkPolyDataWriter.h>
 //==========================
 std::vector<unsigned long> mitk::FiberBundleX::DoExtractFiberIds(mitk::PlanarFigure::Pointer pf)
 {
 
     MITK_INFO << "Extracting fibers!";
     // vector which is returned, contains all extracted FiberIds
     std::vector<unsigned long> FibersInROI;
 
     /* Handle type of planarfigure */
     // if incoming pf is a pfc
     mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast<mitk::PlanarFigureComposite*>(pf.GetPointer());
     if (!pfcomp.IsNull()) {
         // process requested boolean operation of PFC
     } else
     {
 
         mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D();
         const mitk::PlaneGeometry* planeGeometry = dynamic_cast<const mitk::PlaneGeometry*> (pfgeometry.GetPointer());
         Vector3D planeNormal = planeGeometry->GetNormal();
         planeNormal.Normalize();
         Point3D planeOrigin = planeGeometry->GetOrigin();
 
         MITK_INFO << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl;
         MITK_INFO << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl;
 
 
         /* init necessary vectors hosting pointIds and FiberIds */
         // contains all pointIds which are crossing the cutting plane
         std::vector<int> PointsOnPlane;
 
         // based on PointsOnPlane, all ROI relevant point IDs are stored here
         std::vector<int> PointsInROI;
 
 
         /* Define cutting plane by ROI (PlanarFigure) */
         vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
         plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]);
         plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]);
 
         //same plane but opposite normal direction. so point cloud will be reduced -> better performance
         vtkSmartPointer<vtkPlane> planeR = vtkSmartPointer<vtkPlane>::New();
 
         //define new origin along the normal but close to the original one
         // OriginNew = OriginOld + 1*Normal
         //        Vector3D extendedNormal;
         //        int multiplyFactor = 1;
         //        extendedNormal[0] = planeNormal[0] * multiplyFactor;
         //        extendedNormal[1] = planeNormal[1] * multiplyFactor;
         //        extendedNormal[2] = planeNormal[2] * multiplyFactor;
         //        Point3D RplaneOrigin = planeOrigin - extendedNormal;
         //        planeR->SetOrigin(RplaneOrigin[0],RplaneOrigin[1],RplaneOrigin[2]);
         //        planeR->SetNormal(-planeNormal[0],-planeNormal[1],-planeNormal[2]);
         //        MITK_INFO << "RPlaneOrigin: " << RplaneOrigin[0] << " | " << RplaneOrigin[1]
         //                  << " | " << RplaneOrigin[2];
 
         /* get all points/fibers cutting the plane */
         MITK_INFO << "start clipping";
         vtkSmartPointer<vtkClipPolyData> clipper = vtkSmartPointer<vtkClipPolyData>::New();
         clipper->SetInput(m_FiberIdDataSet);
         clipper->SetClipFunction(plane);
         clipper->GenerateClipScalarsOn();
         clipper->GenerateClippedOutputOn();
         vtkSmartPointer<vtkPolyData> clipperout = clipper->GetClippedOutput();
         MITK_INFO << "end clipping";
 
         /* for some reason clipperoutput is not initialized for futher processing
       * so far only writing out clipped polydata provides requested
       */
         //        MITK_INFO << "writing clipper output";
         //        vtkSmartPointer<vtkPolyDataWriter> writerC = vtkSmartPointer<vtkPolyDataWriter>::New();
         //        writerC->SetInput(clipperout1);
         //        writerC->SetFileName("/vtkOutput/Clipping.vtk");
         //        writerC->SetFileTypeToASCII();
         //        writerC->Write();
         //        MITK_INFO << "writing done";
 
         MITK_INFO << "init and update clipperoutput";
         clipperout->GetPointData()->Initialize();
         clipperout->Update();
         MITK_INFO << "init and update clipperoutput completed";
 
         //        MITK_INFO << "start clippingRecursive";
         //        vtkSmartPointer<vtkClipPolyData> Rclipper = vtkSmartPointer<vtkClipPolyData>::New();
         //        Rclipper->SetInput(clipperout1);
         //        Rclipper->SetClipFunction(planeR);
         //        Rclipper->GenerateClipScalarsOn();
         //        Rclipper->GenerateClippedOutputOn();
         //        vtkSmartPointer<vtkPolyData> clipperout = Rclipper->GetClippedOutput();
         //        MITK_INFO << "end clipping recursive";
 
         //        MITK_INFO << "writing clipper output 2";
         //        vtkSmartPointer<vtkPolyDataWriter> writerC1 = vtkSmartPointer<vtkPolyDataWriter>::New();
         //        writerC1->SetInput(clipperout);
         //        writerC1->SetFileName("/vtkOutput/RClipping.vtk");
         //        writerC1->SetFileTypeToASCII();
         //        writerC1->Write();
         //        MITK_INFO << "init and update clipperoutput";
         //        clipperout->GetPointData()->Initialize();
         //        clipperout->Update();
         //        MITK_INFO << "init and update clipperoutput completed";
 
         MITK_INFO << "STEP 1: find all points which have distance 0 to the given plane";
         /*======STEP 1======
       * extract all points, which are crossing the plane */
         // Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index
         vtkSmartPointer<vtkDataArray> distanceList = clipperout->GetPointData()->GetScalars();
         vtkIdType sizeOfList =  distanceList->GetNumberOfTuples();
         PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then!
                                          * size of list can be optimized by reducing allocation, but be aware of iterator and vector size*/
 
         for (int i=0; i<sizeOfList; ++i) {
             double *distance = distanceList->GetTuple(i);
             //std::cout << "distance of point " << i << " : " << distance[0] << std::endl;
 
             // check if point is on plane.
             // 0.01 due to some approximation errors when calculating distance
             if (distance[0] >= -0.01 && distance[0] <= 0.01)
             {
                 //std::cout << "adding " << i << endl;
                 PointsOnPlane.push_back(i); //push back in combination with reserve is fastest way to fill vector with various values
 
                 //optimize: here also check if point is inside radius
 
 
             }
 
         }
 
         // DEBUG print out all interesting points, stop where array starts with value -1. after -1 no more interesting idx are set!
         //        std::vector<int>::iterator rit = PointsOnPlane.begin();
         //        while (rit != PointsOnPlane.end() ) {
         //            std::cout << "interesting point: " << *rit << " coord: " << clipperout->GetPoint(*rit)[0] << " | " <<  clipperout->GetPoint(*rit)[1] << " | " << clipperout->GetPoint(*rit)[2] << endl;
         //            rit++;
         //        }
 
 
         MITK_INFO << "Num Of points on plane: " <<  PointsOnPlane.size();
 
         MITK_INFO << "Step 2: extract Interesting points with respect to given extraction planarFigure";
 
         PointsInROI.reserve(PointsOnPlane.size());
         /*=======STEP 2=====
      * extract ROI relevant pointIds */
 
         mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New();
         mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New();
         if (pf->GetNameOfClass() == circleName->GetNameOfClass() )
         {
 
             //calculate circle radius
             mitk::Point3D V1w = pf->GetWorldControlPoint(0); //centerPoint
             mitk::Point3D V2w  = pf->GetWorldControlPoint(1); //radiusPoint
 
             //calculate distance between those 2 and
             double distPF;
             distPF =  sqrt((double)  (V2w[0] - V1w[0]) * (V2w[0] - V1w[0]) +
                            (V2w[1] - V1w[1]) * (V2w[1] - V1w[1]) +
                            (V2w[2] - V1w[2]) * (V2w[2] - V1w[2]));
 
             //MITK_INFO << "Circle Radius: " << distPF;
 
             for (int i=0; i<PointsOnPlane.size(); i++)
             {
 
                 //                MITK_INFO << clipperout->GetPoint(PointsOnPlane[i])[0] << " - " << V1w[0];
                 //                MITK_INFO << clipperout->GetPoint(PointsOnPlane[i])[1] << " - " << V1w[1];
                 //                MITK_INFO << clipperout->GetPoint(PointsOnPlane[i])[2] << " - " << V1w[2];
 
                 //distance between circle radius and given point
                 double XdistPnt =  sqrt((double) (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) * (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) +
                                         (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) * (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) +
                                         (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2]) * (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2])) ;
 
                 //   MITK_INFO << "PntDistance to Radius: " << XdistPnt;
                 if( XdistPnt <= distPF)
                 {
                     // MITK_INFO << "point in Circle";
                     PointsInROI.push_back(PointsOnPlane[i]);
                 }
 
             }//end for(i)
             // MITK_INFO << "Points inside circle radius: " << PointsInROI.size();
         }
 
         MITK_INFO << "Step3: Identify fibers";
 
         /*======STEP 3=======
      * identify fiberIds for points in ROI */
 
         // we need to access the fiberId Array, so make sure that this array is available
         if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY))
         {
             MITK_INFO << "ERROR: FiberID array does not exist, no correlation between points and fiberIds possible! Make sure calling GenerateFiberIds()";
             return FibersInROI; // FibersInRoi is empty then
         }
 
         // prepare a structure where each point id is represented as an indexId.
         // vector looks like: | pntId | fiberIdx |
         std::vector< unsigned long > pointindexFiberMap;
 
         // walk through the whole subline section and create an vector sorted by point index
         vtkCellArray *clipperlines = clipperout->GetLines();
         clipperlines->InitTraversal();
         long numOfLineCells = clipperlines->GetNumberOfCells();
         unsigned long numofClippedPoints = clipperout->GetNumberOfPoints();
         pointindexFiberMap.reserve(numofClippedPoints);
 
 
         //prepare resulting vector
         FibersInROI.reserve(PointsInROI.size());
 
         MITK_INFO << "\n===== Pointindex based structure initialized ======\n";
 
         // go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id.
         for (int i=0, ic=0 ; i<numOfLineCells; i++, ic+=3)
         { //ic is the index counter for the cells hosting the desired information, eg. 2 | 45 | 46. each cell consits of 3 items.
 
             vtkIdType npts;
             vtkIdType *pts;
             clipperlines->GetCell(ic, npts, pts);
 
             // go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. eg. idx[0]=45; idx[1]=46
             for (long j=0; j<npts; j++)
             {
                 // MITK_INFO << "writing fiber id: " << clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0] << " to pointId: " << pts[j];
                 pointindexFiberMap[ pts[j] ] = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0];
                 // MITK_INFO << "in array: " << pointindexFiberMap[ pts[j] ];
             }
 
         }
 
         MITK_INFO << "\n===== Pointindex based structure finalized ======\n";
 
         // get all Points in ROI with according fiberID
         for (long k = 0; k < PointsInROI.size(); k++)
         {
             // MITK_INFO << "point " << PointsInROI[k] << " belongs to fiber " << pointindexFiberMap[ PointsInROI[k] ];
             FibersInROI.push_back(pointindexFiberMap[ PointsInROI[k] ]);
         }
 
 
 
     }
 
     return FibersInROI;
 }
 
 void mitk::FiberBundleX::UpdateFiberGeometry()
 {
     if (m_NumFibers<=0)
     {
         mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
         geometry->SetImageGeometry(true);
         float b[] = {0, 1, 0, 1, 0, 1};
         geometry->SetFloatBounds(b);
         SetGeometry(geometry);
         return;
     }
     float min = itk::NumericTraits<float>::min();
     float max = itk::NumericTraits<float>::max();
     float b[] = {max, min, max, min, max, min};
 
     vtkCellArray* cells = m_FiberPolyData->GetLines();
     cells->InitTraversal();
     for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
     {
         vtkCell* cell = m_FiberPolyData->GetCell(i);
         int p = cell->GetNumberOfPoints();
         vtkPoints* points = cell->GetPoints();
         for (int j=0; j<p; j++)
         {
             double p[3];
             points->GetPoint(j, p);
 
             if (p[0]<b[0])
                 b[0]=p[0];
             if (p[0]>b[1])
                 b[1]=p[0];
 
             if (p[1]<b[2])
                 b[2]=p[1];
             if (p[1]>b[3])
                 b[3]=p[1];
 
             if (p[2]<b[4])
                 b[4]=p[2];
             if (p[2]>b[5])
                 b[5]=p[2];
         }
     }
 
     // provide some border margin
     for(int i=0; i<=4; i+=2)
         b[i] -=10;
     for(int i=1; i<=5; i+=2)
         b[i] +=10;
 
     mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
     geometry->SetImageGeometry(true);
     geometry->SetFloatBounds(b);
     this->SetGeometry(geometry);
 }
 
 QStringList mitk::FiberBundleX::GetAvailableColorCodings()
 {
     QStringList availableColorCodings;
     int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays();
     for(int i=0; i<numColors; i++)
     {
         availableColorCodings.append(m_FiberPolyData->GetPointData()->GetArrayName(i));
     }
 
     //this controlstructure shall be implemented by the calling method
     if (availableColorCodings.isEmpty())
         MITK_INFO << "no colorcodings available in fiberbundleX";
 
     //    for(int i=0; i<availableColorCodings.size(); i++)
     //    {
     //            MITK_INFO << availableColorCodings.at(i).toLocal8Bit().constData();
     //    }
 
     return availableColorCodings;
 }
 
 
 char* mitk::FiberBundleX::GetCurrentColorCoding()
 {
     return m_currentColorCoding;
 }
 
 void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding)
 {
     if (requestedColorCoding==NULL)
         return;
 
     if(strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 )
     {
         this->m_currentColorCoding = (char*) COLORCODING_ORIENTATION_BASED;
         this->m_isModified = true;
 
     } else if(strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) {
         this->m_currentColorCoding = (char*) COLORCODING_FA_BASED;
         this->m_isModified = true;
     } else {
         MITK_INFO << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure";
         this->m_currentColorCoding = "---"; //will cause blank colorcoding of fibers
         this->m_isModified = true;
     }
 }
 
 bool mitk::FiberBundleX::isFiberBundleXModified()
 {
     return m_isModified;
 }
 void mitk::FiberBundleX::setFBXModificationDone()
 {
     m_isModified = false;
 }
 
 void mitk::FiberBundleX::ResampleFibers()
 {
     mitk::Geometry3D::Pointer geometry = GetGeometry();
     mitk::Vector3D spacing = geometry->GetSpacing();
 
     float minSpacing = 1;
     if(spacing[0]<spacing[1] && spacing[0]<spacing[2])
         minSpacing = spacing[0];
     else if (spacing[1] < spacing[2])
         minSpacing = spacing[1];
     else
         minSpacing = spacing[2];
 
     ResampleFibers(minSpacing);
 }
 
 // Resample fiber to get equidistant points
 void mitk::FiberBundleX::ResampleFibers(float len)
 {
     vtkSmartPointer<vtkPolyData> newPoly = vtkSmartPointer<vtkPolyData>::New();
     vtkSmartPointer<vtkCellArray> newCellArray = vtkSmartPointer<vtkCellArray>::New();
     vtkSmartPointer<vtkPoints>    newPoints = vtkSmartPointer<vtkPoints>::New();
 
     vtkSmartPointer<vtkCellArray> vLines = m_FiberPolyData->GetLines();
     vLines->InitTraversal();
     int numberOfLines = m_NumFibers;
 
     for (int i=0; i<numberOfLines; i++)
     {
         vtkIdType   numPoints(0);
         vtkIdType*  points(NULL);
         vLines->GetNextCell ( numPoints, points );
 
         vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
 
         double* point = m_FiberPolyData->GetPoint(points[0]);
         vtkIdType pointId = newPoints->InsertNextPoint(point);
         container->GetPointIds()->InsertNextId(pointId);
 
         float dtau = 0;
         int cur_p = 1;
         itk::Vector<float,3> dR;
         float normdR = 0;
 
         for (;;)
         {
             while (dtau <= len && cur_p < numPoints)
             {
                 itk::Vector<float,3> v1;
                 point = m_FiberPolyData->GetPoint(points[cur_p-1]);
                 v1[0] = point[0];
                 v1[1] = point[1];
                 v1[2] = point[2];
                 itk::Vector<float,3> v2;
                 point = m_FiberPolyData->GetPoint(points[cur_p]);
                 v2[0] = point[0];
                 v2[1] = point[1];
                 v2[2] = point[2];
 
                 dR  = v2 - v1;
                 normdR = std::sqrt(dR.GetSquaredNorm());
                 dtau += normdR;
                 cur_p++;
             }
 
             if (dtau >= len)
             {
                 itk::Vector<float,3> v1;
                 point = m_FiberPolyData->GetPoint(points[cur_p-1]);
                 v1[0] = point[0];
                 v1[1] = point[1];
                 v1[2] = point[2];
 
                 itk::Vector<float,3> v2 = v1 - dR*( (dtau-len)/normdR );
                 pointId = newPoints->InsertNextPoint(v2.GetDataPointer());
                 container->GetPointIds()->InsertNextId(pointId);
             }
             else
             {
                 point = m_FiberPolyData->GetPoint(points[numPoints-1]);
                 pointId = newPoints->InsertNextPoint(point);
                 container->GetPointIds()->InsertNextId(pointId);
                 break;
             }
             dtau = dtau-len;
         }
 
         newCellArray->InsertNextCell(container);
     }
 
     newPoly->SetPoints(newPoints);
     newPoly->SetLines(newCellArray);
     m_FiberPolyData = newPoly;
     UpdateFiberGeometry();
 }
 
 
 /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
 void mitk::FiberBundleX::UpdateOutputInformation()
 {
 
 }
 void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion()
 {
 
 }
 bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion()
 {
     return false;
 }
 bool mitk::FiberBundleX::VerifyRequestedRegion()
 {
     return true;
 }
 void mitk::FiberBundleX::SetRequestedRegion( itk::DataObject *data )
 {
 
 }