diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkProjectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkProjectionFilter.h
index 163bf99444..501e56c07b 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkProjectionFilter.h
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkProjectionFilter.h
@@ -1,155 +1,158 @@
 /*===================================================================
 
 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 ITKPROJECTIONFILTER_H_
 #define ITKPROJECTIONFILTER_H_
 
 #include "itkObject.h"
 #include "itkImage.h"
 #include "mitkImage.h"
 #include "mitkTbssImage.h"
 
 namespace itk
 {
 
 
 /**
   * \brief Projection part of the TBSS pipeline
   *
   * This class performs the projection step of the TBSS pipeline
   * (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 )
   * As input it takes a binary skeleton, a distance map, and a vector image containing the image gradients
   * that are typically provided by the itkSkeletonizationFilter and the itkDistanceMapFilter.
+  * Furthermore it requires a 4d dataset with patient data registered to the same space as the mean FA image.
+  * This 4D dataset is typically created by the TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index),
+  * in which case it is often named all_FA.nii.gz
   */
 
 
 class ProjectionFilter : public Object
 {
 
 public:
 
   typedef itk::Image<float, 3> RealImageType;
 
   typedef itk::CovariantVector<int,3> VectorType;
 
   typedef itk::Image<VectorType, 3> VectorImageType;
 
   typedef itk::Image<char,3> CharImageType;
 
   typedef itk::Image<float, 4> Float4DImageType;
   typedef itk::Image<float, 3> FloatImageType;
 
 
 
 public:
 
   /** */
   typedef ProjectionFilter Self;
 
   /** Superclass */
   typedef Object Superclass;
 
   /** Smart Pointer */
   typedef SmartPointer<Self> Pointer;
 
   /** Smart Pointer */
   typedef SmartPointer<const Self> ConstPointer;
 
   /** */
   itkNewMacro( Self)
 
 
   /** \brief Does the actual projection */
   void Project();
 
 
   /** \brief Set the distance map
    *
    * Sets the distance map that decodes for every voxel the distance to the nearest point on the skeleton.
    */
   itkSetMacro(DistanceMap, RealImageType::Pointer)
 
 
   /** \brief Set the directions
    *
    * Sets the direction calculated by the TBSS skeletonization algorithm in itkSkeletonizationFilter.
    */
   itkSetMacro(Directions, VectorImageType::Pointer)
 
 
   /** \brief Set the binary skeleton
    *
    * Sets the binary skeleton that defines on which voxels must be projected.
    */
   itkSetMacro(Skeleton, CharImageType::Pointer)
 
 
   /** \brief Set the mask defining tubular structures on the skeleton
    *
    * Sets a binary mask that defines wich part of the white matter skeleton are tubular instead of sheet like.
    * This is important because the a different projection method is used for sheet like structues and
    * tubular structures.
    */
   itkSetMacro(Tube, CharImageType::Pointer)
 
 
   /** \brief Set a 4D image containing the 3D registered FA maps of all study subjects. */
   itkSetMacro(AllFA, Float4DImageType::Pointer)
 
 
   /** \brief Returns a 4D image containing the skeleton projections of all subjects */
   itkGetMacro(Projections, Float4DImageType::Pointer)
 
 
 protected:
 
   /** Constructor */
   ProjectionFilter();
 
   /** Destructor */
   virtual ~ProjectionFilter();
 
   RealImageType::Pointer m_DistanceMap;
 
   VectorImageType::Pointer m_Directions;
 
   CharImageType::Pointer m_Skeleton;
 
   CharImageType::Pointer m_Tube;
 
   Float4DImageType::Pointer m_Projections;
 
   Float4DImageType::Pointer m_AllFA;
 
   int round(float x)
   {
     if (x>0.0) return ((int) (x+0.5));
     else       return ((int) (x-0.5));
   }
 
 protected:
 
 
 
 };
 
 }
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "itkProjectionFilter.txx"
 #endif
 
 #endif
diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h b/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h
index 9a46f4f167..9319c4ce8a 100644
--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h
+++ b/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h
@@ -1,115 +1,118 @@
 /*===================================================================
 
 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 ITKSKELETONIZATIONFILTER_H_
 #define ITKSKELETONIZATIONFILTER_H_
 
 #include "itkImageToImageFilter.h"
 #include "itkImage.h"
 #include "mitkImage.h"
 #include <itkVectorImage.h>
 
 namespace itk
 {
 
 /**
   * \brief Skeletonization part of the TBSS pipeline
   *
-  * This class takes a 3D image (typically the mean FA image as calculated in the standard TBSS pipeline)
-  * and performs the non-maximum-suppression (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 )
+  * This class takes a 3D image which is typically the mean FA image that is calculated after registration by the FSL TBSS pipeline (see
+  * http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index for the user manual) and performs the non-maximum-suppression to create a white matter skeleton.
+  *
+  *
+  * The skeletonization algorithm is described in Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 )
   */
 
 
 template < class TInputImage, class TOutputImage >
 class SkeletonizationFilter : public ImageToImageFilter<TInputImage, TOutputImage>
 {
 
 
 public:
 
   /** Typedef for input ImageType. */
   typedef TInputImage  InputImageType;
 
   typedef itk::CovariantVector<int,3> VectorType;
 
   typedef itk::Image<VectorType, 3> VectorImageType;
 
 
   /** Typedef for output ImageType. */
   typedef TOutputImage OutputImageType;
 
   typedef itk::VectorImage<int, 3> GradientImageType;
 
 
   /** */
   typedef SkeletonizationFilter Self;
 
   /** Superclass */
   typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
 
   typedef SmartPointer<Self> Pointer;
 
   typedef SmartPointer<const Self> ConstPointer;
 
   itkNewMacro( Self)
 
   /** \brief Performs the work */
   virtual void GenerateData();
 
 
   /** \brief Output the gradient image as itkVectorImage
    *
    * Output the gradient image by first converting it to an itk vector image
    */
   GradientImageType::Pointer GetGradientImage();
 
   /** \brief Output the gradient image as an itkImage containing vector */
   VectorImageType::Pointer GetVectorImage()
   {
     return m_DirectionImage;
   }
 
 
 
 
 protected:
 
   SkeletonizationFilter();
 
   virtual ~SkeletonizationFilter();
 
   VectorImageType::Pointer m_DirectionImage;
 
   int round(float x)
   {
     if (x>0.0) return ((int) (x+0.5));
     else       return ((int) (x-0.5));
   }
 
 
 protected:
 
 
 
 };
 
 }
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "itkSkeletonizationFilter.txx"
 #endif
 
 #endif
diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h
index 0f508ca5a6..4e782fc8b3 100644
--- a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h
+++ b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h
@@ -1,152 +1,151 @@
 /*===================================================================
 
 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 __mitkTractAnalyzer_h_
 #define __mitkTractAnalyzer_h_
 
 #include "QuantificationExports.h"
 #include <itkImage.h>
 #include "mitkImage.h"
 #include "mitkImageCast.h"
 
 #include <mitkTbssRoiImage.h>
 #include <mitkPointSet.h>
 
 
 namespace mitk{
 /**
   * \brief Creates a region of interest for tract-specific analysis of existing TBSS data
   *
-  * This class needs a 3D image (typically a mean FA skeleton as produced by the standard TBSS pipeline of FSL)
-  * and a user-defined point set defining the points through which the region of interest should pass.
+  * This class needs a 3D image, which is the mean FA skeleton as produced by the standard TBSS pipeline of FSL.
+  * How this dataset can be obtained can be found in the TBSS user manual: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index
+  * Furthermore, this class requires a user-defined point set defining the points through which the region of interest should pass.
+  * The output is a TBSS roi image, which is a binary images defining the roi and metadata containing indices
+  * that can be used for plotting graphs using the QmitkTbssRoiAnalysisWidget
   */
 
 
 class Quantification_EXPORT TractAnalyzer
 {
 
 public:
 
 
   TractAnalyzer();
   ~TractAnalyzer() {}
 
 
   /** Image type definitions */
   typedef itk::Image<unsigned char,3> CharImageType;
   typedef itk::Image<float,3> FloatImageType;
 
 
   /** \brief Main method for region of interest calculation
    *
    * A region of interest is calculated adding the segments between the points on the ROI
    * that was specified by the user.
    */
   void MakeRoi();
 
 
 
-  /** \brief Sets the input image
-   *
-   * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated
-   * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).
-   */
+  /** \brief Returns the TbssRoiImage **/
   mitk::TbssRoiImage::Pointer GetRoiImage()
   {
     return m_TbssRoi;
   }
 
 
   /** \brief Sets the input image
    *
    * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated
    * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).
    */
   void SetInputImage(mitk::Image::Pointer inputImage)
   {
     m_InputImage = inputImage;
   }
 
 
   /** \brief Sets the user-defined point set
    *
    * Set the user-defined point sets. The region of interest must pass through these points.
    */
   void SetPointSet(mitk::PointSet::Pointer pointSet)
   {
     m_PointSetNode = pointSet;
   }
 
 
   /** \brief Sets a lower bound for the threshold.
    *
    * Low fractional anisotropy values can indicate partial volume of non white matter tissue.
    * This thresholds limits the search for a region of interest to voxels with a minimum value.
    */
   void SetThreshold(double threshold)
   {
     m_Threshold = threshold;
   }
 
 
 
   /** \brief Returns a string with the indices of points on the region of interest
    *
    * The region of interest calculated by the TractAnalyzer contains a list of ITK indices.
    * This method returns a string containing these indices for display in the GUI
    */
   std::string GetPathDescription()
   {
     return m_PathDescription;
   }
 
 protected:
 
 
 
   /** \brief Calculates a segment of the region of interest
    *
    * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated
    * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).
    */
   std::vector< itk::Index<3> > CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint);
 
 
   /** \brief Output TbssRoiImage */
   mitk::TbssRoiImage::Pointer m_TbssRoi;
 
   /** \brief Inputimage */
   mitk::Image::Pointer m_InputImage;
 
   /** \brief Threshold for ROI search */
   double m_Threshold;
 
   /** \brief User defined point set */
   mitk::PointSet::Pointer m_PointSetNode;
 
   /** \brief Path description in as string for display in GUI */
   std::string m_PathDescription;
 
 
 
 private:
 
 };
 
 }
 
 #endif //__itkTractAnalyzer_h_
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h
index 238bd07a6d..f564c2b535 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h
@@ -1,226 +1,229 @@
 /*===================================================================
 
 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 QmitkTbssRoiAnalysisWidget_H_
 #define QmitkTbssRoiAnalysisWidget_H_
 
 #include "QmitkPlotWidget.h"
 
 #include <org_mitk_gui_qt_diffusionimaging_Export.h>
 
 #include <mitkFiberBundleX.h>
 #include <mitkTbssImage.h>
 
 #include <itkVectorImage.h>
 
 typedef itk::VectorImage<float,3>     VectorImageType;
 typedef std::vector< itk::Index<3> > RoiType;
 
 typedef itk::Point<float,3>               PointType;
 typedef std::vector< PointType>           TractType;
 typedef std::vector< TractType > TractContainerType;
 
 class QwtPlotPicker;
 
 /**
  * \brief Plot widget for TBSS Data
- * This widget can plot regions of interest on TBSS projection data.
+ * This widget can plot regions of interest on TBSS projection data. The projection data is created by importing FSL TBSS subject data and
+ * completing it with patient data using the QmitkTractbasedSpatialStatisticsView.
+ * The region of interest is a vector of indices from which data for plotting should be obtained.
  */
+
 class DIFFUSIONIMAGING_EXPORT QmitkTbssRoiAnalysisWidget : public QmitkPlotWidget
 {
 
 Q_OBJECT
 
 public:
 
 
   QmitkTbssRoiAnalysisWidget( QWidget * parent);
   virtual ~QmitkTbssRoiAnalysisWidget();
 
 
-  /* \brief Set group information */
+  /* \brief Set group information as a vector of pairs of group name and number of group members */
   void SetGroups(std::vector< std::pair<std::string, int> > groups)
   {
     m_Groups = groups;
   }
 
   /* \brief Draws the group averaged profiles */
   void DrawProfiles();
 
 
   void PlotFiber4D(mitk::TbssImage::Pointer tbssImage,
                    mitk::FiberBundleX *fib,
                    mitk::PlanarFigure* startRoi,
                    mitk::PlanarFigure* endRoi,
                    int number);
 
 
   void PlotFiberBundles(TractContainerType tracts, mitk::Image* img, bool avg=false);
 
 
   /* \brief Sets the projections of the individual subjects */
   void SetProjections(VectorImageType::Pointer projections)
   {
     m_Projections = projections;
   }
 
   /* \brief Set the region of interest*/
   void SetRoi(RoiType roi)
   {
     m_Roi = roi;
   }
 
   /* \brief Set structure information to display in the plot */
   void SetStructure(std::string structure)
   {
     m_Structure = structure;
   }
 
   /* \brief Set measurement type for display in the plot */
   void SetMeasure(std::string measure)
   {
     m_Measure = measure;
   }
 
   /* \brief Draws a bar to indicate were the user clicked in the plot */
   void drawBar(int x);
 
 
 
   /* \brief Returns the values of the group averaged profiles */
   std::vector <std::vector<double> > GetVals()
   {
     return m_Vals;
   }
 
 
   /* \brief Returns the values of the individual subjects profiles */
   std::vector <std::vector<double> > GetIndividualProfiles()
   {
     return m_IndividualProfiles;
   }
 
 
   std::vector<double> GetAverageProfile()
   {
     return m_Average;
   }
 
 
   void SetPlottingFiber(bool b)
   {
     m_PlottingFiberBundle = b;
   }
 
   bool IsPlottingFiber()
   {
     return m_PlottingFiberBundle;
   }
 
 
   void PlotFiberBetweenRois(mitk::FiberBundleX *fib, mitk::Image* img,
                             mitk::PlanarFigure* startRoi, mitk::PlanarFigure* endRoi, bool avg=-1, int number=25);
 
 
 
 
   // Takes an index which is an x coordinate from the plot and finds the corresponding position in world space
   mitk::Point3D GetPositionInWorld(int index);
   void ModifyPlot(int number, bool avg);
 
 
 
   QwtPlotPicker* m_PlotPicker;
 
 protected:
 
   mitk::FiberBundleX* m_Fib;
 
 
   std::vector< std::vector<double> > m_Vals;
 
   std::vector< std::vector<double> > m_IndividualProfiles;
   std::vector< double > m_Average;
 
 
 
   std::vector< std::vector<double> > CalculateGroupProfiles();
   std::vector< std::vector<double> > CalculateGroupProfilesFibers(mitk::TbssImage::Pointer tbssImage,
                                                                   mitk::FiberBundleX *fib,
                                                                   mitk::PlanarFigure* startRoi,
                                                                   mitk::PlanarFigure* endRoi,
                                                                   int number);
 
   void Plot(std::vector <std::vector<double> > groupProfiles);
 
 
   void Tokenize(const std::string& str,
                 std::vector<std::string>& tokens,
                 const std::string& delimiters = " ")
   {
     // Skip delimiters at beginning.
     std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
     // Find first "non-delimiter".
     std::string::size_type pos     = str.find_first_of(delimiters, lastPos);
 
     while (std::string::npos != pos || std::string::npos != lastPos)
     {
         // Found a token, add it to the vector.
         tokens.push_back(str.substr(lastPos, pos - lastPos));
         // Skip delimiters.  Note the "not_of"
         lastPos = str.find_first_not_of(delimiters, pos);
         // Find next "non-delimiter"
         pos = str.find_first_of(delimiters, lastPos);
     }
   }
 
   std::vector< std::pair<std::string, int> > m_Groups;
 
   VectorImageType::Pointer m_Projections;
   RoiType m_Roi;
   std::string m_Structure;
   std::string m_Measure;
 
   bool m_PlottingFiberBundle; // true when the plot results from a fiber tracking result (vtk .fib file)
 
 
   // Resample a collection of tracts so that every tract contains #number equidistant samples
   TractContainerType ParameterizeTracts(TractContainerType tracts, int number);
 
 
   TractContainerType m_CurrentTracts;
 
 
   mitk::Image* m_CurrentImage;
   mitk::TbssImage* m_CurrentTbssImage;
 
   mitk::PlanarFigure* m_CurrentStartRoi;
   mitk::PlanarFigure* m_CurrentEndRoi;
 
 
   void DoPlotFiberBundles(mitk::FiberBundleX *fib, mitk::Image* img,
                           mitk::PlanarFigure* startRoi, mitk::PlanarFigure* endRoi, bool avg=false, int number=25);
 
 
 
   /* \brief Creates tracts from a mitk::FiberBundleX and two planar figures indicating the start end end point */
   TractContainerType CreateTracts(mitk::FiberBundleX *fib, mitk::PlanarFigure* startRoi, mitk::PlanarFigure* endRoi);
 
 
 
 };
 
 #endif
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 42233fa086..c6a5ce32e3 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h
@@ -1,175 +1,178 @@
 /*===================================================================
 
 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 <QmitkFunctionality.h>
 
 #include "ui_QmitkTractbasedSpatialStatisticsViewControls.h"
 #include <QListWidgetItem>
 
 #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.
+  * for all subjects that are analyzed statistically in a whole-brain manner.
+  * This plugin provides functionality to select single tracts and analyze them separately.
+  *
+  * Prerequisites: the mean_FA_skeleton and all_FA_skeletonised datasets produced by the FSL TBSS pipeline: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index
 */
 
 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 QPointF& 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 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 PlotFiber4D(mitk::TbssImage*, mitk::FiberBundleX* fib, mitk::PlanarFigure* startRoi=NULL, mitk::PlanarFigure* endRoi=NULL);
 
     // 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);
 
     mitk::DataNode::Pointer m_CurrentFiberNode; // needed for the index property when interacting with the plot widget
 
     // 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