diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp
index 88ce4028b2..86f1e19d02 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp
@@ -1,1200 +1,1184 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 // Blueberry
 #include "berryIWorkbenchWindow.h"
 #include "berryIWorkbenchPage.h"
 #include "berryISelectionService.h"
 #include "berryConstants.h"
 #include "berryPlatformUI.h"
 
 // Qmitk
 #include "QmitkTractbasedSpatialStatisticsView.h"
 #include "QmitkStdMultiWidget.h"
 
 #include "mitkDataNodeObject.h"
 #include <itkCastImageFilter.h>
 
 // Qt
 #include <QMessageBox>
 #include <qfiledialog.h>
 #include <QDirIterator>
 #include <QInputDialog>
 #include <QDir>
 #include <QStringList>
 #include <QMessageBox>
 #include <QSortFilterProxyModel>
 #include <QClipboard>
 
 #include <itkNiftiImageIO.h>
 #include <itkImageFileReader.h>
 
 #include <iostream>
 #include <fstream>
 #include <limits>
 
 
 #include <itkMultiplyImageFilter.h>
 #include <mitkTractAnalyzer.h>
 #include <mitkTbssImporter.h>
 #include <mitkProgressBar.h>
 #include <mitkPlanarCircle.h>
 #include <mitkPlanarFigureInteractor.h>
 
 
 #include <mitkVectorImageMapper2D.h>
 #include "vtkFloatArray.h"
 #include "vtkLinearTransform.h"
 #include "vtkPoints.h"
 #include "mitkSurface.h"
 #include <vtkGlyph3D.h>
 #include "vtkArrowSource.h"
 #include "vtkUnstructuredGrid.h"
 #include "vtkPointData.h"
 #include <vtkCellArray.h>
 #include <vtkPolyLine.h>
 
 #include <boost/graph/graph_traits.hpp>
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/dijkstra_shortest_paths.hpp>
 
 #include <QMessageBox>
 
 #include "mitkITKImageImport.h"
 // #include "mitkImageMapperGL2D.h"
 #include "mitkVolumeDataVtkMapper3D.h"
 #include "mitkImageAccessByItk.h"
 #include "mitkTensorImage.h"
 
 #include "itkDiffusionTensor3D.h"
 
 
 #define SEARCHSIGMA 10 // length in linear voxel dimens
 
 #define MAXSEARCHLENGTH (3*SEARCHSIGMA)
 
 const std::string QmitkTractbasedSpatialStatisticsView::VIEW_ID = "org.mitk.views.tractbasedspatialstatistics";
 
 using namespace berry;
 
 
 QmitkTractbasedSpatialStatisticsView::QmitkTractbasedSpatialStatisticsView()
 : QmitkFunctionality()
 , m_Controls( 0 )
 , m_MultiWidget( NULL )
 {
 
 }
 
 QmitkTractbasedSpatialStatisticsView::~QmitkTractbasedSpatialStatisticsView()
 {
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::PerformChange()
 {
   m_Controls->m_RoiPlotWidget->ModifyPlot(m_Controls->m_Segments->value(), m_Controls->m_Average->isChecked());
 }
 
 void QmitkTractbasedSpatialStatisticsView::OnSelectionChanged(std::vector<mitk::DataNode*> nodes)
 {
   //datamanager selection changed
   if (!this->IsActivated())
     return;
 
 
   // Get DataManagerSelection
   if (!this->GetDataManagerSelection().empty())
   {
     mitk::DataNode::Pointer sourceImageNode = this->GetDataManagerSelection().front();
     mitk::Image::Pointer sourceImage = dynamic_cast<mitk::Image*>(sourceImageNode->GetData());
 
     if (!sourceImage)
     {
       m_Controls->m_TbssImageLabel->setText(
         QString( sourceImageNode->GetName().c_str() ) + " is no image"
         );
 
       return;
     }
 
     // set Text
     m_Controls->m_TbssImageLabel->setText(
       QString( sourceImageNode->GetName().c_str() ) + " (" +
       QString::number(sourceImage->GetDimension()) + "D)"
       );
 
 
   }
   else
   {
     m_Controls->m_TbssImageLabel->setText("Please select an image");
   }
 
 
+  // Check which datatypes are selected in the datamanager and enable/disable widgets accordingly
+
   bool foundTbssRoi = false;
   bool foundTbss = false;
   bool found3dImage = false;
   bool found4dImage = false;
   bool foundFiberBundle = false;
   bool foundStartRoi = false;
   bool foundEndRoi = false;
 
   mitk::TbssRoiImage* roiImage;
   mitk::TbssImage* image;
   mitk::Image* img;
   mitk::FiberBundleX* fib;
   mitk::PlanarFigure* start;
   mitk::PlanarFigure* end;
 
   m_CurrentStartRoi = NULL;
   m_CurrentEndRoi = NULL;
 
 
 
   for ( int i=0; i<nodes.size(); i++ )
   {
 
     // only look at interesting types
     // check for valid data
     mitk::BaseData* nodeData = nodes[i]->GetData();
     if( nodeData )
     {
       if(QString("TbssRoiImage").compare(nodeData->GetNameOfClass())==0)
       {
         foundTbssRoi = true;
         roiImage = static_cast<mitk::TbssRoiImage*>(nodeData);
       }
       else if (QString("TbssImage").compare(nodeData->GetNameOfClass())==0)
       {
         foundTbss = true;
         image = static_cast<mitk::TbssImage*>(nodeData);
       }
       else if(QString("Image").compare(nodeData->GetNameOfClass())==0)
       {
         img = static_cast<mitk::Image*>(nodeData);
         if(img->GetDimension() == 3)
         {
           found3dImage = true;
         }
         else if(img->GetDimension() == 4)
         {
           found4dImage = true;
         }
       }
 
       else if (QString("FiberBundleX").compare(nodeData->GetNameOfClass())==0)
       {
         foundFiberBundle = true;
         fib = static_cast<mitk::FiberBundleX*>(nodeData);
         this->m_CurrentFiberNode = nodes[i];
       }
 
 
       if(QString("PlanarCircle").compare(nodeData->GetNameOfClass())==0)
       {
         if(!foundStartRoi)
         {
           start = dynamic_cast<mitk::PlanarFigure*>(nodeData);
           this->m_CurrentStartRoi = nodes[i];
           foundStartRoi =  true;
         }
         else
         {
           end = dynamic_cast<mitk::PlanarFigure*>(nodeData);
           this->m_CurrentEndRoi = nodes[i];
           foundEndRoi = true;
         }
       }
     }
   }
 
 
   this->m_Controls->m_CreateRoi->setEnabled(found3dImage);
   this->m_Controls->m_ImportFsl->setEnabled(found4dImage);
 
 
 
   if(foundTbss && foundTbssRoi)
   {
     this->Plot(image, roiImage);
   }
 
   if(found3dImage && foundFiberBundle && foundStartRoi && foundEndRoi)
   {
     this->PlotFiberBundle(fib, img, start, end);
   }
 
   else if(found3dImage == true && foundFiberBundle)
   {
     this->PlotFiberBundle(fib, img);
   }
 
   if(found3dImage)
   {
     this->InitPointsets();
   }
 
   this->m_Controls->m_Cut->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi);
   this->m_Controls->m_SegmentLabel->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && found3dImage);
   this->m_Controls->m_Segments->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && found3dImage);
   this->m_Controls->m_Average->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && found3dImage);
 
 }
 
 void QmitkTractbasedSpatialStatisticsView::InitPointsets()
 {
   // Check if PointSetStart exsits, if not create it.
   m_P1 = this->GetDefaultDataStorage()->GetNamedNode("PointSetNode");
 
   if (m_PointSetNode)
   {
     //m_PointSetNode = dynamic_cast<mitk::PointSet*>(m_P1->GetData());
     return;
   }
 
   if ((!m_P1) || (!m_PointSetNode))
   {
     // create new ones
     m_PointSetNode = mitk::PointSet::New();
     m_P1 = mitk::DataNode::New();
     m_P1->SetData( m_PointSetNode );
     m_P1->SetProperty( "name", mitk::StringProperty::New( "PointSet" ) );
     m_P1->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) );
     m_P1->SetProperty( "helper object", mitk::BoolProperty::New(true) ); // CHANGE if wanted
     m_P1->SetProperty( "pointsize", mitk::FloatProperty::New( 0.1 ) );
     m_P1->SetColor( 1.0, 0.0, 0.0 );
     this->GetDefaultDataStorage()->Add(m_P1);
     m_Controls->m_PointWidget->SetPointSetNode(m_P1);
     m_Controls->m_PointWidget->SetMultiWidget(GetActiveStdMultiWidget());
   }
 }
 
 void QmitkTractbasedSpatialStatisticsView::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::QmitkTractbasedSpatialStatisticsViewControls;
     m_Controls->setupUi( parent );
     this->CreateConnections();
   }
 
 
-  m_IsInitialized = false;
-
   // Table for the FSL TBSS import
   m_GroupModel = new QmitkTbssTableModel();
   m_Controls->m_GroupInfo->setModel(m_GroupModel);
 
 
 }
 
 void QmitkTractbasedSpatialStatisticsView::Activated()
 {
   QmitkFunctionality::Activated();
 
   berry::ISelection::ConstPointer sel(
     this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager"));
   //m_CurrentSelection = sel.Cast<const IStructuredSelection>();
   //m_SelListener.Cast<TbssSelListener>()->DoSelectionChanged(sel);
 }
 
 void QmitkTractbasedSpatialStatisticsView::Deactivated()
 {
   QmitkFunctionality::Deactivated();
 }
 
 void QmitkTractbasedSpatialStatisticsView::CreateConnections()
 {
   if ( m_Controls )
   {
     connect( (QObject*)(m_Controls->m_CreateRoi), SIGNAL(clicked()), this, SLOT(CreateRoi()) );
     connect( (QObject*)(m_Controls->m_ImportFsl), SIGNAL(clicked()), this, SLOT(TbssImport()) );
     connect( (QObject*)(m_Controls->m_AddGroup), SIGNAL(clicked()), this, SLOT(AddGroup()) );
     connect( (QObject*)(m_Controls->m_RemoveGroup), SIGNAL(clicked()), this, SLOT(RemoveGroup()) );
     connect( (QObject*)(m_Controls->m_Clipboard), SIGNAL(clicked()), this, SLOT(CopyToClipboard()) );
     connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(selected(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) );
     connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(moved(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) );
     connect( (QObject*)(m_Controls->m_Cut), SIGNAL(clicked()), this, SLOT(Cut()) );
     connect( (QObject*)(m_Controls->m_Average), SIGNAL(stateChanged(int)), this, SLOT(PerformChange()) );
     connect( (QObject*)(m_Controls->m_Segments), SIGNAL(valueChanged(int)), this, SLOT(PerformChange()) );
 
   }
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::CopyToClipboard()
 {
 
 
 
   if(m_Controls->m_RoiPlotWidget->IsPlottingFiber())
   {
     // Working with fiber bundles
     std::vector <std::vector<double> > profiles = m_Controls->m_RoiPlotWidget->GetIndividualProfiles();
 
-
-
     QString clipboardText;
     for (std::vector<std::vector<double> >::iterator it = profiles.begin(); it
                                                            != profiles.end(); ++it)
     {
       for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
             (*it).end(); ++it2)
       {
         clipboardText.append(QString("%1 \t").arg(*it2));
       }
       clipboardText.append(QString("\n"));
     }
 
 
 
     if(m_Controls->m_Average->isChecked())
     {
       std::vector<double> averages = m_Controls->m_RoiPlotWidget->GetAverageProfile();
       clipboardText.append(QString("\nAverage\n"));
 
       for (std::vector<double>::iterator it2 = averages.begin(); it2 !=
             averages.end(); ++it2)
       {
         clipboardText.append(QString("%1 \t").arg(*it2));
 
       }
     }
 
     QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
 
   }
 
   else{
 
     // Working with TBSS Data
     if(m_Controls->m_Average->isChecked())
     {
       std::vector<std::vector<double> > vals = m_Controls->m_RoiPlotWidget->GetVals();
       QString clipboardText;
       for (std::vector<std::vector<double> >::iterator it = vals.begin(); it
                                                              != vals.end(); ++it)
       {
         for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
               (*it).end(); ++it2)
         {
           clipboardText.append(QString("%1 \t").arg(*it2));
 
           double d = *it2;
           std::cout << d <<std::endl;
         }
         clipboardText.append(QString("\n"));
       }
 
       QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
     }
     else
     {
       std::vector<std::vector<double> > vals = m_Controls->m_RoiPlotWidget->GetIndividualProfiles();
       QString clipboardText;
       for (std::vector<std::vector<double> >::iterator it = vals.begin(); it
                                                              != vals.end(); ++it)
       {
         for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
               (*it).end(); ++it2)
         {
           clipboardText.append(QString("%1 \t").arg(*it2));
 
           double d = *it2;
           std::cout << d <<std::endl;
         }
         clipboardText.append(QString("\n"));
       }
       QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
     }
 
   }
 
 
 }
 
 void QmitkTractbasedSpatialStatisticsView::RemoveGroup()
 {
 
   QTableView *temp = static_cast<QTableView*>(m_Controls->m_GroupInfo);
  // QSortFilterProxyModel *proxy = static_cast<QSortFilterProxyModel*>(temp->model());
   QItemSelectionModel *selectionModel = temp->selectionModel();
 
   QModelIndexList indices = selectionModel->selectedRows();
 
   QModelIndex index;
 
   foreach(index, indices)
   {
     int row = index.row();
     m_GroupModel->removeRows(row, 1, QModelIndex());
   }
 
 }
 
 
 
 void QmitkTractbasedSpatialStatisticsView::AddGroup()
 {
   QString group("Group");
   int number = 0;
   QPair<QString, int> pair(group, number);
   QList< QPair<QString, int> >list = m_GroupModel->getList();
 
 
   if(!list.contains(pair))
   {
     m_GroupModel->insertRows(0, 1, QModelIndex());
 
     QModelIndex index = m_GroupModel->index(0, 0, QModelIndex());
     m_GroupModel->setData(index, group, Qt::EditRole);
     index = m_GroupModel->index(0, 1, QModelIndex());
     m_GroupModel->setData(index, number, Qt::EditRole);
 
   }
-  else
-  {
-    //QMessageBox::information(this, "Duplicate name");
-  }
-
-
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::TbssImport()
 {
 
   // Read groups from the interface
   mitk::TbssImporter::Pointer importer = mitk::TbssImporter::New();
 
   QList< QPair<QString, int> >list = m_GroupModel->getList();
 
+
   if(list.size() == 0)
   {
     QMessageBox msgBox;
     msgBox.setText("No study group information has been set yet.");
     msgBox.exec();
     return;
   }
 
 
   std::vector < std::pair<std::string, int> > groups;
   for(int i=0; i<list.size(); i++)
   {
     QPair<QString, int> pair = list.at(i);
     std::string s = pair.first.toStdString();
     int n = pair.second;
 
     std::pair<std::string, int> p;
     p.first = s;
     p.second = n;
     groups.push_back(p);
   }
 
   importer->SetGroupInfo(groups);
 
   std::string minfo = m_Controls->m_MeasurementInfo->text().toStdString();
   importer->SetMeasurementInfo(minfo);
 
 
   std::string name = "";
 
   std::vector<mitk::DataNode*> nodes = this->GetDataManagerSelection();
 
   for ( int i=0; i<nodes.size(); i++ )
   {
     if(QString("Image").compare(nodes[i]->GetData()->GetNameOfClass())==0)
     {
       mitk::Image* img = static_cast<mitk::Image*>(nodes[i]->GetData());
       if(img->GetDimension() == 4)
       {
         importer->SetImportVolume(img);
         name = nodes[i]->GetName();
       }
     }
   }
 
 
   mitk::TbssImage::Pointer tbssImage;
 
   tbssImage = importer->Import();
   name += "_tbss";
   AddTbssToDataStorage(tbssImage, name);
 
 
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::AddTbssToDataStorage(mitk::Image* image, std::string name)
 {
   mitk::LevelWindow levelwindow;
   levelwindow.SetAuto( image );
   mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
   levWinProp->SetLevelWindow( levelwindow );
 
   mitk::DataNode::Pointer result = mitk::DataNode::New();
   result->SetProperty( "name", mitk::StringProperty::New(name) );
   result->SetData( image );
   result->SetProperty( "levelwindow", levWinProp );
 
 
   // add new image to data storage and set as active to ease further processing
   GetDefaultDataStorage()->Add( result );
 
   // show the results
   mitk::RenderingManager::GetInstance()->RequestUpdateAll();
 }
 
+
 void QmitkTractbasedSpatialStatisticsView::Clicked(const QwtDoublePoint& pos)
 {
   int index = (int)pos.x();
 
   if(m_Roi.size() > 0 && m_CurrentGeometry != NULL && !m_Controls->m_RoiPlotWidget->IsPlottingFiber() )
   {
 
     index = std::min( (int)m_Roi.size()-1, std::max(0, index) );
     itk::Index<3> ix = m_Roi.at(index);
 
     mitk::Vector3D i;
     i[0] = ix[0];
     i[1] = ix[1];
     i[2] = ix[2];
 
     mitk::Vector3D w;
 
     m_CurrentGeometry->IndexToWorld(i, w);
 
     mitk::Point3D origin = m_CurrentGeometry->GetOrigin();
 
     mitk::Point3D p;
     p[0] = w[0] + origin[0];
     p[1] = w[1] + origin[1];
     p[2] = w[2] + origin[2];
 
     m_MultiWidget->MoveCrossToPosition(p);
     m_Controls->m_RoiPlotWidget->drawBar(index);
   }
 
   else if(m_Controls->m_RoiPlotWidget->IsPlottingFiber() )
   {
 
     mitk::Point3D point = m_Controls->m_RoiPlotWidget->GetPositionInWorld(index);
     m_MultiWidget->MoveCrossToPosition(point);
 
 
   }
 
 
 }
 
 void QmitkTractbasedSpatialStatisticsView::Cut()
 {
   mitk::BaseData* fibData = m_CurrentFiberNode->GetData();
   mitk::FiberBundleX* fib = static_cast<mitk::FiberBundleX*>(fibData);
 
   mitk::BaseData* startData = m_CurrentStartRoi->GetData();
   mitk::PlanarFigure* startRoi = static_cast<mitk::PlanarFigure*>(startData);
   mitk::PlaneGeometry* startGeometry2D = dynamic_cast<mitk::PlaneGeometry*>( const_cast<mitk::Geometry2D*>(startRoi->GetGeometry2D()) );
 
   mitk::BaseData* endData = m_CurrentEndRoi->GetData();
   mitk::PlanarFigure* endRoi = static_cast<mitk::PlanarFigure*>(endData);
   mitk::PlaneGeometry* endGeometry2D = dynamic_cast<mitk::PlaneGeometry*>( const_cast<mitk::Geometry2D*>(endRoi->GetGeometry2D()) );
 
   mitk::Point3D startCenter = startRoi->GetWorldControlPoint(0); //center Point of start roi
   mitk::Point3D endCenter = endRoi->GetWorldControlPoint(0); //center Point of end roi
 
   mitk::FiberBundleX::Pointer inStart = fib->ExtractFiberSubset(startRoi);
   mitk::FiberBundleX::Pointer inBoth = inStart->ExtractFiberSubset(endRoi);
 
   int num = inBoth->GetNumFibers();
 
   vtkSmartPointer<vtkPolyData> fiberPolyData = inBoth->GetFiberPolyData();
   vtkCellArray* lines = fiberPolyData->GetLines();
   lines->InitTraversal();
 
 
   // initialize new vtk polydata
   vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
   vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
   vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
 
   int pointIndex=0;
 
 
   // find start and endpoint
   for( int fiberID( 0 ); fiberID < num; fiberID++ )
   {
     vtkIdType   numPointsInCell(0);
     vtkIdType*  pointsInCell(NULL);
     lines->GetNextCell ( numPointsInCell, pointsInCell );
 
     int startId = 0;
     int endId = 0;
 
     float minDistStart = std::numeric_limits<float>::max();
     float minDistEnd = std::numeric_limits<float>::max();
 
 
     vtkSmartPointer<vtkPolyLine> polyLine = vtkSmartPointer<vtkPolyLine>::New();
     int lineIndex=0;
 
 
     for( int pointInCellID( 0 ); pointInCellID < numPointsInCell ; pointInCellID++)
     {
       double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
 
       mitk::Point3D point;
       point[0] = p[0];
       point[1] = p[1];
       point[2] = p[2];
 
       float distanceToStart = point.EuclideanDistanceTo(startCenter);
       float distanceToEnd = point.EuclideanDistanceTo(endCenter);
 
       if(distanceToStart < minDistStart)
       {
         minDistStart = distanceToStart;
         startId = pointInCellID;
       }
 
       if(distanceToEnd < minDistEnd)
       {
         minDistEnd = distanceToEnd;
         endId = pointInCellID;
       }
 
 
 
     }
 
 
 
     /* We found the start and end points of of the part that should be plottet for
        the current fiber. now we need to plot them. If the endId is smaller than the startId the plot order
        must be reversed*/
 
     if(startId < endId)
     {
 
       double *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
 
       mitk::Vector3D p0;
       p0[0] = p[0];
       p0[1] = p[1];
       p0[2] = p[2];
 
       p = fiberPolyData->GetPoint( pointsInCell[ startId+1 ] );
 
       mitk::Vector3D p1;
       p1[0] = p[0];
       p1[1] = p[1];
       p1[2] = p[2];
 
 
       // Check if p and p2 are both on the same side of the plane
       mitk::Vector3D normal = startGeometry2D->GetNormal();
 
       mitk::Point3D pStart;
       pStart[0] = p0[0];
       pStart[1] = p0[1];
       pStart[2] = p0[2];
 
       bool startOnPositive = startGeometry2D->IsAbove(pStart);
 
       mitk::Point3D pSecond;
       pSecond[0] = p1[0];
       pSecond[1] = p1[1];
       pSecond[2] = p1[2];
 
       bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
 
 
       // Calculate intersection with the plane
 
       mitk::Vector3D onPlane;
       onPlane[0] = startCenter[0];
       onPlane[1] = startCenter[1];
       onPlane[2] = startCenter[2];
 
 
       if(! (secondOnPositive ^ startOnPositive) )
       {
         /* startId and startId+1 lie on the same side of the plane, so we need
            need startId-1 to calculate the intersection with the planar figure*/
         p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
         p1[0] = p[0];
         p1[1] = p[1];
         p1[2] = p[2];
       }
 
 
       double d = ( (onPlane-p0)*normal) / ( (p0-p1) * normal );
 
       mitk::Vector3D newPoint = (p0-p1);
 
       newPoint[0] = d*newPoint[0] + p0[0];
       newPoint[1] = d*newPoint[1] + p0[1];
       newPoint[2] = d*newPoint[2] + p0[2];
 
 
       double insertPoint[3];
       insertPoint[0] = newPoint[0];
       insertPoint[1] = newPoint[1];
       insertPoint[2] = newPoint[2];
 
 
       // First insert the intersection with the start roi
       points->InsertNextPoint(insertPoint);
       polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
       lineIndex++;
       pointIndex++;
 
       if(! (secondOnPositive ^ startOnPositive) )
       {
         /* StartId and startId+1 lie on the same side of the plane
            so startId is also part of the ROI*/
 
         double *start = fiberPolyData->GetPoint( pointsInCell[startId] );
         points->InsertNextPoint(start);
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
 
 
       }
 
       // Insert the rest up and to including endId-1
       for( int pointInCellID( startId+1 ); pointInCellID < endId ; pointInCellID++)
       {
         // create new polyline for new polydata
         double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
         points->InsertNextPoint(p);
 
 
         // add point to line
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
 
       }
 
 
 
       /* endId must be included if endId and endId-1 lie on the same side of the
          plane defined by endRoi*/
 
 
       p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
       p0[0] = p[0];      p0[1] = p[1];      p0[2] = p[2];
 
 
       p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
       p1[0] = p[0];      p1[1] = p[1];      p1[2] = p[2];
 
 
       mitk::Point3D pLast;
       pLast[0] = p0[0];      pLast[1] = p0[1];      pLast[2] = p0[2];
 
       mitk::Point3D pBeforeLast;
       pBeforeLast[0] = p1[0];      pBeforeLast[1] = p1[1];      pBeforeLast[2] = p1[2];
 
       bool lastOnPositive = endGeometry2D->IsAbove(pLast);
       bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
       normal = endGeometry2D->GetNormal();
 
 
       onPlane[0] = endCenter[0];
       onPlane[1] = endCenter[1];
       onPlane[2] = endCenter[2];
 
 
 
       if(! (lastOnPositive ^ secondLastOnPositive) )
       {
         /* endId and endId-1 lie on the same side of the plane, so we need
            need endId+1 to calculate the intersection with the planar figure.
            this should exist since we know that the fiber crosses the planar figure
            endId is part of the roi so can also be included here*/
         p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
         p1[0] = p[0];
         p1[1] = p[1];
         p1[2] = p[2];
 
 
         double *end = fiberPolyData->GetPoint( pointsInCell[endId] );
         points->InsertNextPoint(end);
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
       }
 
       d = ( (onPlane-p0)*normal) / ( (p0-p1) * normal );
 
       newPoint = (p0-p1);
 
       newPoint[0] = d*newPoint[0] + p0[0];
       newPoint[1] = d*newPoint[1] + p0[1];
       newPoint[2] = d*newPoint[2] + p0[2];
 
       insertPoint[0] = newPoint[0];
       insertPoint[1] = newPoint[1];
       insertPoint[2] = newPoint[2];
 
       //Insert the Last Point (intersection with the end roi)
 
       points->InsertNextPoint(insertPoint);
       polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
       lineIndex++;
       pointIndex++;
 
 
     }
 
     // Need to reverse walking order
     else{
       double *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
 
       mitk::Vector3D p0;
       p0[0] = p[0];
       p0[1] = p[1];
       p0[2] = p[2];
 
       p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
 
       mitk::Vector3D p1;
       p1[0] = p[0];
       p1[1] = p[1];
       p1[2] = p[2];
 
 
       // Check if p and p2 are both on the same side of the plane
       mitk::Vector3D normal = startGeometry2D->GetNormal();
 
       mitk::Point3D pStart;
       pStart[0] = p0[0];
       pStart[1] = p0[1];
       pStart[2] = p0[2];
 
       bool startOnPositive = startGeometry2D->IsAbove(pStart);
 
       mitk::Point3D pSecond;
       pSecond[0] = p1[0];
       pSecond[1] = p1[1];
       pSecond[2] = p1[2];
 
       bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
 
 
       // Calculate intersection with the plane
 
       mitk::Vector3D onPlane;
       onPlane[0] = startCenter[0];
       onPlane[1] = startCenter[1];
       onPlane[2] = startCenter[2];
 
 
       if(! (secondOnPositive ^ startOnPositive) )
       {
         /* startId and startId-1 lie on the same side of the plane, so we need
            need startId+1 to calculate the intersection with the planar figure*/
         p = fiberPolyData->GetPoint( pointsInCell[ startId+1 ] );
         p1[0] = p[0];
         p1[1] = p[1];
         p1[2] = p[2];
       }
 
 
       double d = ( (onPlane-p0)*normal) / ( (p0-p1) * normal );
 
       mitk::Vector3D newPoint = (p0-p1);
 
       newPoint[0] = d*newPoint[0] + p0[0];
       newPoint[1] = d*newPoint[1] + p0[1];
       newPoint[2] = d*newPoint[2] + p0[2];
 
 
       double insertPoint[3];
       insertPoint[0] = newPoint[0];
       insertPoint[1] = newPoint[1];
       insertPoint[2] = newPoint[2];
 
 
       // First insert the intersection with the start roi
       points->InsertNextPoint(insertPoint);
       polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
       lineIndex++;
       pointIndex++;
 
       if(! (secondOnPositive ^ startOnPositive) )
       {
         /* startId and startId-1 lie on the same side of the plane
            so endId is also part of the ROI*/
 
         double *start = fiberPolyData->GetPoint( pointsInCell[startId] );
         points->InsertNextPoint(start);
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
 
 
       }
 
       // Insert the rest up and to including endId-1
       for( int pointInCellID( startId-1 ); pointInCellID > endId ; pointInCellID--)
       {
         // create new polyline for new polydata
         double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
         points->InsertNextPoint(p);
 
 
         // add point to line
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
 
       }
 
 
 
       /* startId must be included if startId and startId+ lie on the same side of the
          plane defined by endRoi*/
 
 
       p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
       p0[0] = p[0];
       p0[1] = p[1];
       p0[2] = p[2];
 
 
       p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
       p1[0] = p[0];
       p1[1] = p[1];
       p1[2] = p[2];
 
 
       mitk::Point3D pLast;
       pLast[0] = p0[0];
       pLast[1] = p0[1];
       pLast[2] = p0[2];
 
       bool lastOnPositive = endGeometry2D->IsAbove(pLast);
 
       mitk::Point3D pBeforeLast;
       pBeforeLast[0] = p1[0];
       pBeforeLast[1] = p1[1];
       pBeforeLast[2] = p1[2];
 
       bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
 
       onPlane[0] = endCenter[0];
       onPlane[1] = endCenter[1];
       onPlane[2] = endCenter[2];
 
 
 
       if(! (lastOnPositive ^ secondLastOnPositive) )
       {
         /* endId and endId+1 lie on the same side of the plane, so we need
            need endId-1 to calculate the intersection with the planar figure.
            this should exist since we know that the fiber crosses the planar figure*/
         p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
         p1[0] = p[0];
         p1[1] = p[1];
         p1[2] = p[2];
 
 
         /* endId and endId+1 lie on the same side of the plane
            so startId is also part of the ROI*/
 
         double *end = fiberPolyData->GetPoint( pointsInCell[endId] );
         points->InsertNextPoint(end);
         polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
         lineIndex++;
         pointIndex++;
       }
 
       d = ( (onPlane-p0)*normal) / ( (p0-p1) * normal );
 
       newPoint = (p0-p1);
 
       newPoint[0] = d*newPoint[0] + p0[0];
       newPoint[1] = d*newPoint[1] + p0[1];
       newPoint[2] = d*newPoint[2] + p0[2];
 
 
       insertPoint[0] = newPoint[0];
       insertPoint[1] = newPoint[1];
       insertPoint[2] = newPoint[2];
 
 
 
       //Insert the Last Point (intersection with the end roi)
       points->InsertNextPoint(insertPoint);
       polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
       lineIndex++;
       pointIndex++;
 
 
 
     }
 
 
     // add polyline to vtk cell array
      cells->InsertNextCell(polyLine);
 
   }
 
 
   // Add the points to the dataset
   polyData->SetPoints(points);
 
   // Add the lines to the dataset
   polyData->SetLines(cells);
 
   mitk::FiberBundleX::Pointer cutBundle = mitk::FiberBundleX::New(polyData);
 
 
   mitk::DataNode::Pointer cutNode = mitk::DataNode::New();
   cutNode->SetData(cutBundle);
   std::string name = "fiberCut";
   cutNode->SetName(name);
   GetDataStorage()->Add(cutNode);
 
 
 
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
 {
   m_MultiWidget = &stdMultiWidget;
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetNotAvailable()
 {
   m_MultiWidget = NULL;
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::CreateRoi()
 {
-
-  // It is important to load the MeanFASkeletonMask image in MITK to make sure that point selection and
-  // pathfinding is done on the same image
-  //string filename = m_TbssWorkspaceManager.GetInputDir().toStdString() + "/stats/" + m_TbssWorkspaceManager.GetMeanFASkeletonMask().toStdString();
-
-  // Implement a way to obtain skeleton and skeletonFA without sml workspace
-
   bool ok;
   double threshold = QInputDialog::getDouble(m_Controls->m_CreateRoi, tr("Set an FA threshold"),
                                                       tr("Threshold:"), 0.2, 0.0, 1.0, 2, &ok);
 
   if(!ok)
     return;
 
   mitk::Image::Pointer image;
 
-
   std::vector<mitk::DataNode*> nodes = this->GetDataManagerSelection();
 
   for ( int i=0; i<nodes.size(); i++ )
   {
     if(QString("Image").compare(nodes[i]->GetData()->GetNameOfClass())==0)
     {
         mitk::Image* img = static_cast<mitk::Image*>(nodes[i]->GetData());
         if(img->GetDimension() == 3)
         {
           image = img;
         }
     }
   }
 
-
-
   if(image.IsNull())
   {
     return;
   }
 
   mitk::TractAnalyzer analyzer;
   analyzer.SetInputImage(image);
   analyzer.SetThreshold(threshold);
 
   // Set Pointset to analyzer
   analyzer.SetPointSet(m_PointSetNode);
 
   // Run Analyzer
   analyzer.MakeRoi();
 
   // Obtain tbss roi image from analyzer
   mitk::TbssRoiImage::Pointer tbssRoi = analyzer.GetRoiImage();
 
   tbssRoi->SetStructure(m_Controls->m_Structure->text().toStdString());
 
   // get path description and set to interface
   std::string pathDescription = analyzer.GetPathDescription();
   m_Controls->m_PathTextEdit->setPlainText(QString(pathDescription.c_str()));
 
 
   // Add roi image to datastorage
   AddTbssToDataStorage(tbssRoi, m_Controls->m_RoiName->text().toStdString());
 
 
 
 
 }
 
 
 
 void QmitkTractbasedSpatialStatisticsView:: PlotFiberBundle(mitk::FiberBundleX *fib, mitk::Image* img,
                                                            mitk::PlanarFigure* startRoi, mitk::PlanarFigure* endRoi)
 {
   bool avg = m_Controls->m_Average->isChecked();
   int segments = m_Controls->m_Segments->value();
   m_Controls->m_RoiPlotWidget->PlotFiberBetweenRois(fib, img, startRoi ,endRoi, avg, segments);
   m_Controls->m_RoiPlotWidget->SetPlottingFiber(true);
   mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll();
 }
 
 
 void QmitkTractbasedSpatialStatisticsView::Plot(mitk::TbssImage* image, mitk::TbssRoiImage* roiImage)
 {
   if(m_Controls->m_TabWidget->currentWidget() == m_Controls->m_MeasureTAB)
   {
 
     std::vector< itk::Index<3> > roi = roiImage->GetRoi();
     m_Roi = roi;
     m_CurrentGeometry = image->GetGeometry();
 
 
     std::string resultfile = "";
     std::string structure = roiImage->GetStructure();
 
     m_Controls->m_RoiPlotWidget->SetGroups(image->GetGroupInfo());
     m_Controls->m_RoiPlotWidget->SetProjections(image->GetImage());
     m_Controls->m_RoiPlotWidget->SetRoi(roi);
     m_Controls->m_RoiPlotWidget->SetStructure(structure);
     m_Controls->m_RoiPlotWidget->SetMeasure( image->GetMeasurementInfo() );
     m_Controls->m_RoiPlotWidget->DrawProfiles(resultfile);
   }
 
   m_Controls->m_RoiPlotWidget->SetPlottingFiber(false);
 
 }
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h
index dc484f0809..0f3a45cfff 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h
@@ -1,177 +1,170 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 #ifndef QmitkTractbasedSpatialStatisticsView_h
 #define QmitkTractbasedSpatialStatisticsView_h
 
 
-#include <berryISelectionListener.h>
-#include <berryIPartListener.h>
-#include <berryIStructuredSelection.h>
-
-
 #include <QmitkFunctionality.h>
 
 #include "ui_QmitkTractbasedSpatialStatisticsViewControls.h"
 #include <QListWidgetItem>
 
-#include <mitkDiffusionImage.h>
-#include <string>
-
 #include <itkImageFileReader.h>
 #include <itkImageFileWriter.h>
 #include <mitkDataNodeFactory.h>
 
 #include <itkDiffusionTensor3D.h>
 
 #include <mitkTbssImage.h>
 #include <mitkTbssRoiImage.h>
 
 #include "QmitkTbssTableModel.h"
 #include "QmitkTbssMetaTableModel.h"
 
 #include <mitkFiberBundleX.h>
 
 
 // Image types
 typedef short DiffusionPixelType;
 typedef itk::Image<char, 3> CharImageType;
 typedef itk::Image<unsigned char, 3> UCharImageType;
 typedef itk::Image<float, 4> Float4DImageType;
 typedef itk::Image<float, 3> FloatImageType;
 typedef itk::VectorImage<float, 3> VectorImageType;
 
 // Readers/Writers
 typedef itk::ImageFileReader< CharImageType > CharReaderType;
 typedef itk::ImageFileReader< UCharImageType > UCharReaderType;
 typedef itk::ImageFileWriter< CharImageType > CharWriterType;
 typedef itk::ImageFileReader< FloatImageType > FloatReaderType;
 typedef itk::ImageFileWriter< FloatImageType > FloatWriterType;
 typedef itk::ImageFileReader< Float4DImageType > Float4DReaderType;
 typedef itk::ImageFileWriter< Float4DImageType > Float4DWriterType;
 
 
 
 /*!
   * \brief This plugin provides an extension for Tract-based spatial statistics (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024)
   * TBSS enables analyzing the brain by a pipeline of registration, skeletonization, and projection that results in a white matter skeleton
   * for all subjects that are analyzed statistically. This plugin provides functionality to select single tracts and analyze them seperately.
 */
 
 class QmitkTractbasedSpatialStatisticsView : public QmitkFunctionality
 {
 
   Q_OBJECT
 
   public:
 
     static const std::string VIEW_ID;
 
     QmitkTractbasedSpatialStatisticsView();
     virtual ~QmitkTractbasedSpatialStatisticsView();
 
     virtual void CreateQtPartControl(QWidget *parent);
 
     /// \brief Creation of the connections of main and control widget
     virtual void CreateConnections();
 
     virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget);
     virtual void StdMultiWidgetNotAvailable();
 
     /// \brief Called when the functionality is activated
     virtual void Activated();
 
     virtual void Deactivated();
 
 
   protected slots:
 
     // Creates Roi
     void CreateRoi();
 
     void Clicked(const QwtDoublePoint& pos);
 
     // Import of FSL TBSS data
     void TbssImport();
 
     // Add a group as metadata. This metadata is required by the plotting functionality
     void AddGroup();
 
     // Remove a group
     void RemoveGroup();
 
     // Copies the values displayed in the plot widget to clipboard, i.e. exports the data
     void CopyToClipboard();
 
     // Method to cut away parts of fiber bundles that should not be plotted.
     void Cut();
 
-    // Adjust plot
+    // Adjust plot widget
     void PerformChange();
 
 
   protected:
 
 
     /// \brief called by QmitkFunctionality when DataManager's selection has changed
     virtual void OnSelectionChanged( std::vector<mitk::DataNode*> nodes );
 
+    // Creates a plot using a 4D image containing the projections of all subjects and a region of interest
     void Plot(mitk::TbssImage*, mitk::TbssRoiImage*);
 
-    void PlotFiberBundle(mitk::FiberBundleX* fib, mitk::Image* img, mitk::PlanarFigure* startRoi=NULL, mitk::PlanarFigure* endRoi=NULL);
 
-    void InitPointsets();
+    void PlotFiberBundle(mitk::FiberBundleX* fib, mitk::Image* img, mitk::PlanarFigure* startRoi=NULL, mitk::PlanarFigure* endRoi=NULL);
 
-    void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name);
 
-    bool m_IsInitialized;
+    // Create a point set. This point set defines the points through which a region of interest should go
+    void InitPointsets();
 
+    // Pointset and DataNode to contain the PointSet used in ROI creation
     mitk::PointSet::Pointer m_PointSetNode;
     mitk::DataNode::Pointer m_P1;
 
+    // GUI widgets
     Ui::QmitkTractbasedSpatialStatisticsViewControls* m_Controls;
 
+    /* A pointer to the QmitkStdMultiWidget. Used for interaction with the plot widget
+    (clicking in the plot widget makes the image cross jump to the corresponding location
+    on the skeleton).*/
     QmitkStdMultiWidget* m_MultiWidget;
 
-
+    // Used to save the region of interest in a vector of itk::index.
     std::vector< itk::Index<3> > m_Roi;
 
     mitk::FiberBundleX* m_Fib;
 
     mitk::Geometry3D* m_CurrentGeometry;
 
+    // A table model for saving group information in a name,number pair.
     QmitkTbssTableModel* m_GroupModel;
 
-
+    // Convenience function for adding a new image to the datastorage and giving it a name.
     void AddTbssToDataStorage(mitk::Image* image, std::string name);
 
-
-    VectorImageType::Pointer ConvertToVectorImage(mitk::Image::Pointer mitkImg);
-
-
     mitk::DataNode::Pointer m_CurrentFiberNode; // needed for the index property when interacting with the plot widget
 
-    mitk::DataNode::Pointer m_CurrentStartRoi; // needed when a plot should only show values between a start end end roi
-
-    mitk::DataNode::Pointer m_CurrentEndRoi; // idem dito
-
+    // needed when a plot should only show values between a start end end roi
+    mitk::DataNode::Pointer m_CurrentStartRoi;
+    mitk::DataNode::Pointer m_CurrentEndRoi;
 
 };
 
 
 
 #endif // _QMITKTRACTBASEDSPATIALSTATISTICSVIEW_H_INCLUDED