mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract )
{
  ImageLabelPairType labelpair;

   {// Note: .fib image tracts are safed using index coordinates
    mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
    mitk::Point3D firstElementSegCoord, lastElementSegCoord;
    itk::Index<3> firstElementSegIndex, lastElementSegIndex;

    if( singleTract->front().Size() != 3 )
    {
      MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
    }
    for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
    {
      firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
      lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
    }

    // convert from fiber index coordinates to segmentation index coordinates
    FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
    FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );

    for( int index = 0; index < 3; index++ )
    {
      firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
      lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
    }

    int firstLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
    int lastLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];

    labelpair.first = firstLabel;
    labelpair.second = lastLabel;

    // Add property to property map
    CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
    CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
  }

  return labelpair;
}
mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabelAvoidingWhiteMatter( TractType::Pointer singleTract )
{
  ImageLabelPairType labelpair;

  {// Note: .fib image tracts are safed using index coordinates
    mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
    mitk::Point3D firstElementSegCoord, lastElementSegCoord;
    itk::Index<3> firstElementSegIndex, lastElementSegIndex;

    if( singleTract->front().Size() != 3 )
    {
      MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
    }
    for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
    {
      firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
      lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
    }

    // convert from fiber index coordinates to segmentation index coordinates
    FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
    FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );

    for( int index = 0; index < 3; index++ )
    {
      firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
      lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
    }

    int firstLabel = m_SegmentationItk->GetPixel(firstElementSegIndex);
    int lastLabel = m_SegmentationItk->GetPixel(lastElementSegIndex );

    // Check whether the labels belong to the white matter (which means, that the fibers ended early)
    bool extendFront(false), extendEnd(false), retractFront(false), retractEnd(false);
    extendFront = !IsNonWhiteMatterLabel( firstLabel );
    extendEnd = !IsNonWhiteMatterLabel( lastLabel );
    retractFront = IsBackgroundLabel( firstLabel );
    retractEnd = IsBackgroundLabel( lastLabel );

    //if( extendFront || extendEnd )
    //{
    //MBI_INFO << "Before Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
    //}
    if ( extendFront )
    {
      std::vector< int > indexVectorOfPointsToUse;

      //Use first two points for direction
      indexVectorOfPointsToUse.push_back( 1 );
      indexVectorOfPointsToUse.push_back( 0 );

      // label and coordinate temp storage
      int tempLabel( firstLabel );
      itk::Index<3> tempIndex = firstElementSegIndex;

      LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );

      firstLabel = tempLabel;
      firstElementSegIndex = tempIndex;

    }

    if ( extendEnd )
    {
      std::vector< int > indexVectorOfPointsToUse;

      //Use last two points for direction
      indexVectorOfPointsToUse.push_back( singleTract->Size() - 2 );
      indexVectorOfPointsToUse.push_back( singleTract->Size() - 1 );

      // label and coordinate temp storage
      int tempLabel( lastLabel );
      itk::Index<3> tempIndex = lastElementSegIndex;

      LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );

      lastLabel = tempLabel;
      lastElementSegIndex = tempIndex;
    }
        if ( retractFront )
    {
      // label and coordinate temp storage
      int tempLabel( firstLabel );
      itk::Index<3> tempIndex = firstElementSegIndex;

      RetractionUntilBrainMatter( true, singleTract, tempLabel, tempIndex );

      firstLabel = tempLabel;
      firstElementSegIndex = tempIndex;

    }

    if ( retractEnd )
    {
      // label and coordinate temp storage
      int tempLabel( lastLabel );
      itk::Index<3> tempIndex = lastElementSegIndex;

      RetractionUntilBrainMatter( false, singleTract, tempLabel, tempIndex );

      lastLabel = tempLabel;
      lastElementSegIndex = tempIndex;
    }
    //if( extendFront || extendEnd )
    //{
    //    MBI_INFO << "After Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
    //}

    labelpair.first = firstLabel;
    labelpair.second = lastLabel;

    // Add property to property map
    CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
    CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
  }

  return labelpair;
}
mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract )
{
  ImageLabelPairType labelpair;

   {// Note: .fib image tracts are safed using index coordinates
    mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
    mitk::Point3D firstElementSegCoord, lastElementSegCoord;
    mitk::Index3D firstElementSegIndex, lastElementSegIndex;

    if( singleTract->front().Size() != 3 )
    {
      MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
    }
    for( int index = 0; index < singleTract->front().Size(); index++ )
    {
      firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
      lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
    }

    // convert from fiber index coordinates to segmentation index coordinates
    FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
    FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );

    for( int index = 0; index < 3; index++ )
    {
      firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
      lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
    }

    int firstLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
    int lastLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];

    labelpair.first = firstLabel;
    labelpair.second = lastLabel;

    // Add property to property map
    if( ! ( m_LabelToNodePropertyMap.count( firstLabel ) > 0 ) )
    {
      NetworkNode firstNode;

      firstNode.coordinates.resize( 3 );
      for( unsigned int index = 0; index < firstNode.coordinates.size() ; index++ )
      {
        firstNode.coordinates[ index ] = firstElementSegIndex[ index ] ;
      }

      firstNode.label = LabelToString( firstLabel );

      m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( firstLabel, firstNode ) );
    }

    if( ! ( m_LabelToNodePropertyMap.count( lastLabel ) > 0 ) )
    {
      NetworkNode lastNode;

      lastNode.coordinates.resize( 3 );
      for( unsigned int index = 0; index < lastNode.coordinates.size() ; index++ )
      {
        lastNode.coordinates[ index ] = lastElementSegIndex[ index ] ; 
      }

      lastNode.label = LabelToString( lastLabel );

      m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( lastLabel, lastNode ) );
    }
  }

  return labelpair;
}