diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp
index cffb9d5557..9348436a3d 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp
@@ -1,246 +1,247 @@
 /*===================================================================
 
 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 __itkKspaceImageFilter_txx
 #define __itkKspaceImageFilter_txx
 
 #include <time.h>
 #include <stdio.h>
 #include <stdlib.h>
 
 #include "itkKspaceImageFilter.h"
 #include <itkImageRegionConstIterator.h>
 #include <itkImageRegionConstIteratorWithIndex.h>
 #include <itkImageRegionIterator.h>
 #include <itkImageFileWriter.h>
 
 #define _USE_MATH_DEFINES
 #include <math.h>
 
 namespace itk {
 
 template< class TPixelType >
 KspaceImageFilter< TPixelType >
 ::KspaceImageFilter()
     : m_tLine(1)
     , m_kOffset(0)
     , m_FrequencyMap(NULL)
     , m_SimulateRelaxation(true)
     , m_SimulateEddyCurrents(false)
     , m_Tau(70)
     , m_EddyGradientMagnitude(30)
     , m_IsBaseline(true)
     , m_SignalScale(1)
     , m_Spikes(0)
     , m_SpikeAmplitude(1)
     , m_UseConstantRandSeed(false)
 {
     m_DiffusionGradientDirection.Fill(0.0);
 
     m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
     m_RandGen->SetSeed();
 }
 
 template< class TPixelType >
 void KspaceImageFilter< TPixelType >
 ::BeforeThreadedGenerateData()
 {
     if (m_UseConstantRandSeed)  // always generate the same random numbers?
         m_RandGen->SetSeed(0);
     else
         m_RandGen->SetSeed();
 
     typename OutputImageType::Pointer outputImage = OutputImageType::New();
     itk::ImageRegion<2> region; region.SetSize(0, m_OutSize[0]);  region.SetSize(1, m_OutSize[1]);
     outputImage->SetLargestPossibleRegion( region );
     outputImage->SetBufferedRegion( region );
     outputImage->SetRequestedRegion( region );
     outputImage->Allocate();
 
     m_TEMPIMAGE = InputImageType::New();
     m_TEMPIMAGE->SetLargestPossibleRegion( region );
     m_TEMPIMAGE->SetBufferedRegion( region );
     m_TEMPIMAGE->SetRequestedRegion( region );
     m_TEMPIMAGE->Allocate();
 
     m_SimulateDistortions = true;
     if (m_FrequencyMap.IsNull())
     {
         m_SimulateDistortions = false;
         m_FrequencyMap = InputImageType::New();
         m_FrequencyMap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
         m_FrequencyMap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
         m_FrequencyMap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
         m_FrequencyMap->Allocate();
         m_FrequencyMap->FillBuffer(0);
     }
 
     double gamma = 42576000;    // Gyromagnetic ratio in Hz/T
     if (m_DiffusionGradientDirection.GetNorm()>0.001)
     {
         m_EddyGradientMagnitude /= 1000; // eddy gradient magnitude in T/m
         m_DiffusionGradientDirection.Normalize();
         m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_EddyGradientMagnitude *  gamma;
         m_IsBaseline = false;
     }
 
     this->SetNthOutput(0, outputImage);
 }
 
 template< class TPixelType >
 void KspaceImageFilter< TPixelType >
 ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId)
 {
     typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
 
     ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
 
     typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
 
     double kxMax = outputImage->GetLargestPossibleRegion().GetSize(0);  // k-space size in x-direction
     double kyMax = outputImage->GetLargestPossibleRegion().GetSize(1);  // k-space size in y-direction
     double xMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); // scanner coverage in x-direction
     double yMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); // scanner coverage in y-direction
 
     double numPix = kxMax*kyMax;
     double dt = m_tLine/kxMax;
     double fromMaxEcho = - m_tLine*kyMax/2;
 
     double upsampling = xMax/kxMax;     //  discrepany between k-space resolution and image resolution
     double yMaxFov = kyMax*upsampling;  //  actual FOV in y-direction (in x-direction xMax==FOV)
 
     int xRingingOffset = xMax-kxMax;
     int yRingingOffset = yMaxFov-kyMax;
 
     vcl_complex<double> spike(0,0);
     while( !oit.IsAtEnd() )
     {
         itk::Index< 2 > kIdx;
         kIdx[0] = oit.GetIndex()[0];
         kIdx[1] = oit.GetIndex()[1];
 
         double t = fromMaxEcho + ((double)kIdx[1]*kxMax+(double)kIdx[0])*dt;    // dephasing time
 
         // rearrange slice
         if( kIdx[0] <  kxMax/2 )
             kIdx[0] = kIdx[0] + kxMax/2;
         else
             kIdx[0] = kIdx[0] - kxMax/2;
 
         if( kIdx[1] <  kyMax/2 )
             kIdx[1] = kIdx[1] + kyMax/2;
         else
             kIdx[1] = kIdx[1] - kyMax/2;
 
         // calculate eddy current decay factors
         double eddyDecay = 0;
         if (m_SimulateEddyCurrents)
             eddyDecay = exp(-(m_TE/2 + t)/m_Tau) * t/1000;
 
         // calcualte signal relaxation factors
         std::vector< double > relaxFactor;
         if (m_SimulateRelaxation)
             for (unsigned int i=0; i<m_CompartmentImages.size(); i++)
                 relaxFactor.push_back(exp(-(m_TE+t)/m_T2.at(i) -fabs(t)/m_Tinhom));
 
         double kx = kIdx[0];
         double ky = kIdx[1];
         if (oit.GetIndex()[1]%2 == 1)               // reverse readout direction and add ghosting
         {
             kIdx[0] = kxMax-kIdx[0]-1;                // reverse readout direction
             kx = (double)kIdx[0]-m_kOffset;    // add gradient delay induced offset
         }
         else
             kx += m_kOffset;    // add gradient delay induced offset
 
         // add gibbs ringing offset (cropps k-space)
         if (kx>=kxMax/2)
             kx += xRingingOffset;
         if (ky>=kyMax/2)
             ky += yRingingOffset;
 
         vcl_complex<double> s(0,0);
         InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
         while( !it.IsAtEnd() )
         {
             double x = it.GetIndex()[0]-xMax/2;
             double y = it.GetIndex()[1]-yMax/2;
 
             vcl_complex<double> f(0, 0);
 
             // sum compartment signals and simulate relaxation
             for (unsigned int i=0; i<m_CompartmentImages.size(); i++)
                 if (m_SimulateRelaxation)
                     f += std::complex<double>( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_SignalScale, 0);
                 else
                     f += std::complex<double>( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_SignalScale );
 
             // simulate eddy currents and other distortions
             double omega_t = 0;
             if ( m_SimulateEddyCurrents && !m_IsBaseline)
             {
                 itk::Vector< double, 3 > pos; pos[0] = x; pos[1] = y; pos[2] = m_Z;
                 pos = m_DirectionMatrix*pos/1000;   // vector from image center to current position (in meter)
                 omega_t += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2])*eddyDecay;
             }
             if (m_SimulateDistortions)
                 omega_t += m_FrequencyMap->GetPixel(it.GetIndex())*t/1000;
 
             if (y<-yMaxFov/2)
                 y += yMaxFov;
             else if (y>=yMaxFov/2)
                 y -= yMaxFov;
 
             // actual DFT term
             s += f * exp( std::complex<double>(0, 2 * M_PI * (kx*x/xMax + ky*y/yMaxFov + omega_t )) );
 
             ++it;
         }
         s /= numPix;
 
         if (m_Spikes>0 && sqrt(s.imag()*s.imag()+s.real()*s.real()) > sqrt(spike.imag()*spike.imag()+spike.real()*spike.real()) )
             spike = s;
 
         //        m_TEMPIMAGE->SetPixel(kIdx, sqrt(s.real()*s.real()+s.imag()*s.imag()));
         outputImage->SetPixel(kIdx, s);
         ++oit;
     }
 
     spike *= m_SpikeAmplitude;
     for (int i=0; i<m_Spikes; i++)
     {
         itk::Index< 2 > spikeIdx;
         spikeIdx[0] = m_RandGen->GetIntegerVariate()%(int)kxMax;
         spikeIdx[1] = m_RandGen->GetIntegerVariate()%(int)kyMax;
+        MITK_INFO << "Spike at (" << spikeIdx[0] << "," << spikeIdx[1] << ") - Amplitude: " << sqrt(spike.imag()*spike.imag()+spike.real()*spike.real());
         outputImage->SetPixel(spikeIdx, spike);
     }
 
     //    typedef itk::ImageFileWriter< InputImageType > WriterType;
     //    typename WriterType::Pointer writer = WriterType::New();
     //    writer->SetFileName("/local/kspace.nrrd");
     //    writer->SetInput(m_TEMPIMAGE);
     //    writer->Update();
 }
 
 template< class TPixelType >
 void KspaceImageFilter< TPixelType >
 ::AfterThreadedGenerateData()
 {
 
 }
 
 }
 #endif
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
index 12acaee9d2..e49329f948 100755
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
@@ -1,989 +1,991 @@
 /*===================================================================
 
 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.
 
 ===================================================================*/
 
 #include "itkTractsToDWIImageFilter.h"
 #include <boost/progress.hpp>
 #include <vtkSmartPointer.h>
 #include <vtkPolyData.h>
 #include <vtkCellArray.h>
 #include <vtkPoints.h>
 #include <vtkPolyLine.h>
 #include <itkImageRegionIteratorWithIndex.h>
 #include <itkResampleImageFilter.h>
 #include <itkNearestNeighborInterpolateImageFunction.h>
 #include <itkBSplineInterpolateImageFunction.h>
 #include <itkCastImageFilter.h>
 #include <itkImageFileWriter.h>
 #include <itkRescaleIntensityImageFilter.h>
 #include <itkWindowedSincInterpolateImageFunction.h>
 #include <itkResampleDwiImageFilter.h>
 #include <itkKspaceImageFilter.h>
 #include <itkDftImageFilter.h>
 #include <itkAddImageFilter.h>
 #include <itkConstantPadImageFilter.h>
 #include <itkCropImageFilter.h>
 #include <mitkAstroStickModel.h>
 #include <vtkTransform.h>
 #include <iostream>
 #include <fstream>
 #include <itkImageDuplicator.h>
 #include <boost/lexical_cast.hpp>
 
 namespace itk
 {
 
 template< class PixelType >
 TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter()
     : m_CircleDummy(false)
     , m_VolumeAccuracy(10)
     , m_AddGibbsRinging(false)
     , m_NumberOfRepetitions(1)
     , m_EnforcePureFiberVoxels(false)
     , m_InterpolationShrink(1000)
     , m_FiberRadius(0)
     , m_SignalScale(25)
     , m_kOffset(0)
     , m_tLine(1)
     , m_UseInterpolation(false)
     , m_SimulateRelaxation(true)
     , m_tInhom(50)
     , m_TE(100)
     , m_FrequencyMap(NULL)
     , m_EddyGradientStrength(0.001)
     , m_SimulateEddyCurrents(false)
     , m_Spikes(0)
     , m_Wrap(1.0)
     , m_NoiseModel(NULL)
     , m_SpikeAmplitude(1)
     , m_AddMotionArtifact(false)
     , m_UseConstantRandSeed(false)
 {
     m_Spacing.Fill(2.5); m_Origin.Fill(0.0);
     m_DirectionMatrix.SetIdentity();
     m_ImageRegion.SetSize(0, 10);
     m_ImageRegion.SetSize(1, 10);
     m_ImageRegion.SetSize(2, 10);
 
     m_MaxTranslation.Fill(0.0);
     m_MaxRotation.Fill(0.0);
 
     m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
     m_RandGen->SetSeed();
 }
 
 template< class PixelType >
 TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter()
 {
 
 }
 
 template< class PixelType >
 TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images )
 {
     // create slice object
     ImageRegion<2> sliceRegion;
     sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
     sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
     Vector< double, 2 > sliceSpacing;
     sliceSpacing[0] = m_UpsampledSpacing[0];
     sliceSpacing[1] = m_UpsampledSpacing[1];
 
     // frequency map slice
     SliceType::Pointer fMapSlice = NULL;
     if (m_FrequencyMap.IsNotNull())
     {
         fMapSlice = SliceType::New();
         ImageRegion<2> region;
         region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
         region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
         fMapSlice->SetLargestPossibleRegion( region );
         fMapSlice->SetBufferedRegion( region );
         fMapSlice->SetRequestedRegion( region );
         fMapSlice->Allocate();
         fMapSlice->FillBuffer(0.0);
     }
 
     DoubleDwiType::Pointer newImage = DoubleDwiType::New();
     newImage->SetSpacing( m_Spacing );
     newImage->SetOrigin( m_Origin );
     newImage->SetDirection( m_DirectionMatrix );
     newImage->SetLargestPossibleRegion( m_ImageRegion );
     newImage->SetBufferedRegion( m_ImageRegion );
     newImage->SetRequestedRegion( m_ImageRegion );
     newImage->SetVectorLength( images.at(0)->GetVectorLength() );
     newImage->Allocate();
 
     MatrixType transform = m_DirectionMatrix;
     for (int i=0; i<3; i++)
         for (int j=0; j<3; j++)
         {
             if (j<2)
                 transform[i][j] *= m_UpsampledSpacing[j];
             else
                 transform[i][j] *= m_Spacing[j];
         }
 
     std::vector< unsigned int > spikeVolume;
     for (int i=0; i<m_Spikes; i++)
         spikeVolume.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetVectorLength());
     std::sort (spikeVolume.begin(), spikeVolume.end());
     std::reverse (spikeVolume.begin(), spikeVolume.end());
 
     m_StatusText += "0%   10   20   30   40   50   60   70   80   90   100%\n";
     m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
     unsigned long lastTick = 0;
 
     boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2));
     for (unsigned int g=0; g<images.at(0)->GetVectorLength(); g++)
     {
         std::vector< int > spikeSlice;
         while (!spikeVolume.empty() && spikeVolume.back()==g)
         {
             spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2));
             spikeVolume.pop_back();
         }
         std::sort (spikeSlice.begin(), spikeSlice.end());
         std::reverse (spikeSlice.begin(), spikeSlice.end());
 
         for (unsigned int z=0; z<images.at(0)->GetLargestPossibleRegion().GetSize(2); z++)
         {
             std::vector< SliceType::Pointer > compartmentSlices;
             std::vector< double > t2Vector;
 
             for (unsigned int i=0; i<images.size(); i++)
             {
                 DiffusionSignalModel<double>* signalModel;
                 if (i<m_FiberModels.size())
                     signalModel = m_FiberModels.at(i);
                 else
                     signalModel = m_NonFiberModels.at(i-m_FiberModels.size());
 
                 SliceType::Pointer slice = SliceType::New();
                 slice->SetLargestPossibleRegion( sliceRegion );
                 slice->SetBufferedRegion( sliceRegion );
                 slice->SetRequestedRegion( sliceRegion );
                 slice->SetSpacing(sliceSpacing);
                 slice->Allocate();
                 slice->FillBuffer(0.0);
 
                 // extract slice from channel g
                 for (unsigned int y=0; y<images.at(0)->GetLargestPossibleRegion().GetSize(1); y++)
                     for (unsigned int x=0; x<images.at(0)->GetLargestPossibleRegion().GetSize(0); x++)
                     {
                         SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y;
                         DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
 
                         slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]);
 
                         if (fMapSlice.IsNotNull() && i==0)
                             fMapSlice->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D));
                     }
 
                 compartmentSlices.push_back(slice);
                 t2Vector.push_back(signalModel->GetT2());
             }
 
             if (this->GetAbortGenerateData())
                 return NULL;
 
             // create k-sapce (inverse fourier transform slices)
             itk::Size<2> outSize; outSize.SetElement(0, m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_ImageRegion.GetSize(1));
             itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New();
             idft->SetCompartmentImages(compartmentSlices);
             idft->SetT2(t2Vector);
             idft->SetUseConstantRandSeed(m_UseConstantRandSeed);
             idft->SetkOffset(m_kOffset);
             idft->SettLine(m_tLine);
             idft->SetTE(m_TE);
             idft->SetTinhom(m_tInhom);
             idft->SetSimulateRelaxation(m_SimulateRelaxation);
             idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents);
             idft->SetEddyGradientMagnitude(m_EddyGradientStrength);
             idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0);
             idft->SetDirectionMatrix(transform);
             idft->SetDiffusionGradientDirection(m_FiberModels.at(0)->GetGradientDirection(g));
             idft->SetFrequencyMap(fMapSlice);
             idft->SetSignalScale(m_SignalScale);
             idft->SetOutSize(outSize);
             int numSpikes = 0;
             while (!spikeSlice.empty() && spikeSlice.back()==z)
             {
                 numSpikes++;
                 spikeSlice.pop_back();
             }
+            if (numSpikes>0)
+                MITK_INFO << "Gradient " << g << ", Slice " << z << ", Num. peaks " << numSpikes;
             idft->SetSpikes(numSpikes);
             idft->SetSpikeAmplitude(m_SpikeAmplitude);
             idft->Update();
 
             ComplexSliceType::Pointer fSlice;
             fSlice = idft->GetOutput();
 
             ++disp;
             unsigned long newTick = 50*disp.count()/disp.expected_count();
             for (int tick = 0; tick<(newTick-lastTick); tick++)
                 m_StatusText += "*";
             lastTick = newTick;
 
             // fourier transform slice
             SliceType::Pointer newSlice;
             itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New();
             dft->SetInput(fSlice);
             dft->Update();
             newSlice = dft->GetOutput();
 
             // put slice back into channel g
             for (unsigned int y=0; y<fSlice->GetLargestPossibleRegion().GetSize(1); y++)
                 for (unsigned int x=0; x<fSlice->GetLargestPossibleRegion().GetSize(0); x++)
                 {
                     DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
                     SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y;
 
                     DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D);
                     pix3D[g] = newSlice->GetPixel(index2D);
                     newImage->SetPixel(index3D, pix3D);
                 }
             ++disp;
             newTick = 50*disp.count()/disp.expected_count();
             for (int tick = 0; tick<(newTick-lastTick); tick++)
                 m_StatusText += "*";
             lastTick = newTick;
         }
     }
     m_StatusText += "\n\n";
     return newImage;
 }
 
 template< class PixelType >
 void TractsToDWIImageFilter< PixelType >::GenerateData()
 {
     m_StartTime = clock();
     m_StatusText = "Starting simulation\n";
 
     // check input data
     if (m_FiberBundle.IsNull())
         itkExceptionMacro("Input fiber bundle is NULL!");
 
     int numFibers = m_FiberBundle->GetNumFibers();
     if (numFibers<=0)
         itkExceptionMacro("Input fiber bundle contains no fibers!");
 
     if (m_FiberModels.empty())
         itkExceptionMacro("No diffusion model for fiber compartments defined!");
 
     if (m_EnforcePureFiberVoxels)
         while (m_FiberModels.size()>1)
             m_FiberModels.pop_back();
 
     if (m_NonFiberModels.empty())
         itkExceptionMacro("No diffusion model for non-fiber compartments defined!");
 
     int baselineIndex = m_FiberModels[0]->GetFirstBaselineIndex();
     if (baselineIndex<0)
         itkExceptionMacro("No baseline index found!");
 
     if (m_UseConstantRandSeed)  // always generate the same random numbers?
         m_RandGen->SetSeed(0);
     else
         m_RandGen->SetSeed();
 
     // initialize output dwi image
     ImageRegion<3> croppedRegion = m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Wrap);
     itk::Point<double,3> shiftedOrigin = m_Origin; shiftedOrigin[1] += (m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Spacing[1]/2;
 
     typename OutputImageType::Pointer outImage = OutputImageType::New();
     outImage->SetSpacing( m_Spacing );
     outImage->SetOrigin( shiftedOrigin );
     outImage->SetDirection( m_DirectionMatrix );
     outImage->SetLargestPossibleRegion( croppedRegion );
     outImage->SetBufferedRegion( croppedRegion );
     outImage->SetRequestedRegion( croppedRegion );
     outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
     outImage->Allocate();
     typename OutputImageType::PixelType temp;
     temp.SetSize(m_FiberModels[0]->GetNumGradients());
     temp.Fill(0.0);
     outImage->FillBuffer(temp);
 
     // ADJUST GEOMETRY FOR FURTHER PROCESSING
     // is input slize size a power of two?
     unsigned int x=m_ImageRegion.GetSize(0); unsigned int y=m_ImageRegion.GetSize(1);
     ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0;
     m_ImageRegion.SetSize(0, x+pad[0]);
     m_ImageRegion.SetSize(1, y+pad[1]);
     if (m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0))
     {
         itk::ConstantPadImageFilter<ItkDoubleImgType, ItkDoubleImgType>::Pointer zeroPadder = itk::ConstantPadImageFilter<ItkDoubleImgType, ItkDoubleImgType>::New();
         zeroPadder->SetInput(m_FrequencyMap);
         zeroPadder->SetConstant(0);
         zeroPadder->SetPadUpperBound(pad);
         zeroPadder->Update();
         m_FrequencyMap = zeroPadder->GetOutput();
     }
     if (m_TissueMask.IsNotNull() && (pad[0]>0 || pad[1]>0))
     {
         itk::ConstantPadImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer zeroPadder = itk::ConstantPadImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
         zeroPadder->SetInput(m_TissueMask);
         zeroPadder->SetConstant(0);
         zeroPadder->SetPadUpperBound(pad);
         zeroPadder->Update();
         m_TissueMask = zeroPadder->GetOutput();
     }
 
     // apply in-plane upsampling
     double upsampling = 1;
     if (m_AddGibbsRinging)
         upsampling = 2;
     m_UpsampledSpacing = m_Spacing;
     m_UpsampledSpacing[0] /= upsampling;
     m_UpsampledSpacing[1] /= upsampling;
     m_UpsampledImageRegion = m_ImageRegion;
     m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*upsampling);
     m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*upsampling);
     m_UpsampledOrigin = m_Origin;
     m_UpsampledOrigin[0] -= m_Spacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2;
     m_UpsampledOrigin[1] -= m_Spacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2;
     m_UpsampledOrigin[2] -= m_Spacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2;
 
     // generate double images to store the individual compartment signals
     std::vector< DoubleDwiType::Pointer > compartments;
     for (unsigned int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
     {
         DoubleDwiType::Pointer doubleDwi = DoubleDwiType::New();
         doubleDwi->SetSpacing( m_UpsampledSpacing );
         doubleDwi->SetOrigin( m_UpsampledOrigin );
         doubleDwi->SetDirection( m_DirectionMatrix );
         doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion );
         doubleDwi->SetBufferedRegion( m_UpsampledImageRegion );
         doubleDwi->SetRequestedRegion( m_UpsampledImageRegion );
         doubleDwi->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
         doubleDwi->Allocate();
         DoubleDwiType::PixelType pix;
         pix.SetSize(m_FiberModels[0]->GetNumGradients());
         pix.Fill(0.0);
         doubleDwi->FillBuffer(pix);
         compartments.push_back(doubleDwi);
     }
 
     // initialize volume fraction images
     m_VolumeFractions.clear();
     for (unsigned int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
     {
         ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New();
         doubleImg->SetSpacing( m_UpsampledSpacing );
         doubleImg->SetOrigin( m_UpsampledOrigin );
         doubleImg->SetDirection( m_DirectionMatrix );
         doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion );
         doubleImg->SetBufferedRegion( m_UpsampledImageRegion );
         doubleImg->SetRequestedRegion( m_UpsampledImageRegion );
         doubleImg->Allocate();
         doubleImg->FillBuffer(0);
         m_VolumeFractions.push_back(doubleImg);
     }
 
     // resample mask image and frequency map to fit upsampled geometry
     if (m_AddGibbsRinging)
     {
         if (m_TissueMask.IsNotNull())
         {
             // rescale mask image (otherwise there are problems with the resampling)
             itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::Pointer rescaler = itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::New();
             rescaler->SetInput(0,m_TissueMask);
             rescaler->SetOutputMaximum(100);
             rescaler->SetOutputMinimum(0);
             rescaler->Update();
 
             // resample mask image
             itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer resampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
             resampler->SetInput(rescaler->GetOutput());
             resampler->SetOutputParametersFromImage(m_TissueMask);
             resampler->SetSize(m_UpsampledImageRegion.GetSize());
             resampler->SetOutputSpacing(m_UpsampledSpacing);
             resampler->SetOutputOrigin(m_UpsampledOrigin);
             resampler->Update();
             m_TissueMask = resampler->GetOutput();
         }
         // resample frequency map
         if (m_FrequencyMap.IsNotNull())
         {
             itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::Pointer resampler = itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::New();
             resampler->SetInput(m_FrequencyMap);
             resampler->SetOutputParametersFromImage(m_FrequencyMap);
             resampler->SetSize(m_UpsampledImageRegion.GetSize());
             resampler->SetOutputSpacing(m_UpsampledSpacing);
             resampler->SetOutputOrigin(m_UpsampledOrigin);
             resampler->Update();
             m_FrequencyMap = resampler->GetOutput();
         }
     }
 
     // no input tissue mask is set -> create default
     bool maskImageSet = true;
     if (m_TissueMask.IsNull())
     {
         m_StatusText += "No tissue mask set\n";
         MITK_INFO << "No tissue mask set";
         m_TissueMask = ItkUcharImgType::New();
         m_TissueMask->SetSpacing( m_UpsampledSpacing );
         m_TissueMask->SetOrigin( m_UpsampledOrigin );
         m_TissueMask->SetDirection( m_DirectionMatrix );
         m_TissueMask->SetLargestPossibleRegion( m_UpsampledImageRegion );
         m_TissueMask->SetBufferedRegion( m_UpsampledImageRegion );
         m_TissueMask->SetRequestedRegion( m_UpsampledImageRegion );
         m_TissueMask->Allocate();
         m_TissueMask->FillBuffer(1);
         maskImageSet = false;
     }
     else
     {
         m_StatusText += "Using tissue mask\n";
         MITK_INFO << "Using tissue mask";
     }
 
     m_ImageRegion = croppedRegion;
     x=m_ImageRegion.GetSize(0); y=m_ImageRegion.GetSize(1);
     if ( x%2 == 1 )
         m_ImageRegion.SetSize(0, x+1);
     if ( y%2 == 1 )
         m_ImageRegion.SetSize(1, y+1);
 
     // resample fiber bundle for sufficient voxel coverage
     m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n";
     double segmentVolume = 0.0001;
     float minSpacing = 1;
     if(m_UpsampledSpacing[0]<m_UpsampledSpacing[1] && m_UpsampledSpacing[0]<m_UpsampledSpacing[2])
         minSpacing = m_UpsampledSpacing[0];
     else if (m_UpsampledSpacing[1] < m_UpsampledSpacing[2])
         minSpacing = m_UpsampledSpacing[1];
     else
         minSpacing = m_UpsampledSpacing[2];
     FiberBundleType fiberBundle = m_FiberBundle->GetDeepCopy();
     fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy);
     double mmRadius = m_FiberRadius/1000;
     if (mmRadius>0)
         segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy;
 
     double interpFact = 2*atan(-0.5*m_InterpolationShrink);
     double maxVolume = 0;
     double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2];
 
     if (m_AddMotionArtifact)
     {
         if (m_RandomMotion)
         {
             m_StatusText += "Adding random motion artifacts:\n";
             m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast<std::string>(m_MaxRotation) + "°\n";
             m_StatusText += "Maximum translation: +/-" + boost::lexical_cast<std::string>(m_MaxTranslation) + "mm\n";
         }
         else
         {
             m_StatusText += "Adding linear motion artifacts:\n";
             m_StatusText += "Maximum rotation: " + boost::lexical_cast<std::string>(m_MaxRotation) + "°\n";
             m_StatusText += "Maximum translation: " + boost::lexical_cast<std::string>(m_MaxTranslation) + "mm\n";
         }
         MITK_INFO << "Adding motion artifacts";
         MITK_INFO << "Maximum rotation: " << m_MaxRotation;
         MITK_INFO << "Maxmimum translation: " << m_MaxTranslation;
     }
     maxVolume = 0;
 
     m_StatusText += "\n"+this->GetTime()+" > Generating signal of " + boost::lexical_cast<std::string>(m_FiberModels.size()) + " fiber compartments\n";
     MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments";
     boost::progress_display disp(numFibers*m_FiberModels.at(0)->GetNumGradients());
 
     ofstream logFile;
     logFile.open("fiberfox_motion.log");
     logFile << "0 rotation: 0,0,0; translation: 0,0,0\n";
 
     // get transform for motion artifacts
     FiberBundleType fiberBundleTransformed = fiberBundle;
     VectorType rotation = m_MaxRotation/m_FiberModels.at(0)->GetNumGradients();
     VectorType translation = m_MaxTranslation/m_FiberModels.at(0)->GetNumGradients();
 
     // creat image to hold transformed mask (motion artifact)
     ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New();
     itk::ImageDuplicator<ItkUcharImgType>::Pointer duplicator = itk::ImageDuplicator<ItkUcharImgType>::New();
     duplicator->SetInputImage(m_TissueMask);
     duplicator->Update();
     tempTissueMask = duplicator->GetOutput();
 
     // second upsampling needed for motion artifacts
     ImageRegion<3>                      upsampledImageRegion = m_UpsampledImageRegion;
     itk::Vector<double,3>               upsampledSpacing = m_UpsampledSpacing;
     upsampledSpacing[0] /= 4;
     upsampledSpacing[1] /= 4;
     upsampledSpacing[2] /= 4;
     upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4);
     upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4);
     upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4);
     itk::Point<double,3> upsampledOrigin = m_UpsampledOrigin;
     upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2;
     upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2;
     upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2;
     ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New();
     itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer upsampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
     upsampler->SetInput(m_TissueMask);
     upsampler->SetOutputParametersFromImage(m_TissueMask);
     upsampler->SetSize(upsampledImageRegion.GetSize());
     upsampler->SetOutputSpacing(upsampledSpacing);
     upsampler->SetOutputOrigin(upsampledOrigin);
     itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType>::Pointer nn_interpolator
             = itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType>::New();
     upsampler->SetInterpolator(nn_interpolator);
     upsampler->Update();
     upsampledTissueMask = upsampler->GetOutput();
 
     m_StatusText += "0%   10   20   30   40   50   60   70   80   90   100%\n";
     m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
     unsigned int lastTick = 0;
 
     for (int g=0; g<m_FiberModels.at(0)->GetNumGradients(); g++)
     {
         vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData();
 
         ItkDoubleImgType::Pointer intraAxonalVolume = ItkDoubleImgType::New();
         intraAxonalVolume->SetSpacing( m_UpsampledSpacing );
         intraAxonalVolume->SetOrigin( m_UpsampledOrigin );
         intraAxonalVolume->SetDirection( m_DirectionMatrix );
         intraAxonalVolume->SetLargestPossibleRegion( m_UpsampledImageRegion );
         intraAxonalVolume->SetBufferedRegion( m_UpsampledImageRegion );
         intraAxonalVolume->SetRequestedRegion( m_UpsampledImageRegion );
         intraAxonalVolume->Allocate();
         intraAxonalVolume->FillBuffer(0);
 
         // generate fiber signal
         for( int i=0; i<numFibers; i++ )
         {
             vtkCell* cell = fiberPolyData->GetCell(i);
             int numPoints = cell->GetNumberOfPoints();
             vtkPoints* points = cell->GetPoints();
 
             if (numPoints<2)
                 continue;
 
             for( int j=0; j<numPoints; j++)
             {
                 if (this->GetAbortGenerateData())
                 {
                     m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
                     return;
                 }
 
                 double* temp = points->GetPoint(j);
                 itk::Point<float, 3> vertex = GetItkPoint(temp);
                 itk::Vector<double> v = GetItkVector(temp);
 
                 itk::Vector<double, 3> dir(3);
                 if (j<numPoints-1)
                     dir = GetItkVector(points->GetPoint(j+1))-v;
                 else
                     dir = v-GetItkVector(points->GetPoint(j-1));
 
                 if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2])
                     continue;
 
                 itk::Index<3> idx;
                 itk::ContinuousIndex<float, 3> contIndex;
                 tempTissueMask->TransformPhysicalPointToIndex(vertex, idx);
                 tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
 
                 if (!m_UseInterpolation)    // use nearest neighbour interpolation
                 {
                     if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0)
                         continue;
 
                     // generate signal for each fiber compartment
                     for (unsigned int k=0; k<m_FiberModels.size(); k++)
                     {
                         DoubleDwiType::Pointer doubleDwi = compartments.at(k);
                         m_FiberModels[k]->SetFiberDirection(dir);
                         DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx);
                         pix[g] += segmentVolume*m_FiberModels[k]->SimulateMeasurement(g);
                         doubleDwi->SetPixel(idx, pix );
                         double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume;
                         intraAxonalVolume->SetPixel(idx, vol );
 
                         if (g==0 && vol>maxVolume)
                             maxVolume = vol;
                     }
                     continue;
                 }
 
                 double frac_x = contIndex[0] - idx[0]; double frac_y = contIndex[1] - idx[1]; double frac_z = contIndex[2] - idx[2];
                 if (frac_x<0)
                 {
                     idx[0] -= 1;
                     frac_x += 1;
                 }
                 if (frac_y<0)
                 {
                     idx[1] -= 1;
                     frac_y += 1;
                 }
                 if (frac_z<0)
                 {
                     idx[2] -= 1;
                     frac_z += 1;
                 }
 
                 frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5;
                 frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5;
                 frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5;
 
                 // use trilinear interpolation
                 itk::Index<3> newIdx;
                 for (int x=0; x<2; x++)
                 {
                     frac_x = 1-frac_x;
                     for (int y=0; y<2; y++)
                     {
                         frac_y = 1-frac_y;
                         for (int z=0; z<2; z++)
                         {
                             frac_z = 1-frac_z;
 
                             newIdx[0] = idx[0]+x;
                             newIdx[1] = idx[1]+y;
                             newIdx[2] = idx[2]+z;
 
                             double frac = frac_x*frac_y*frac_z;
 
                             // is position valid?
                             if (!tempTissueMask->GetLargestPossibleRegion().IsInside(newIdx) || tempTissueMask->GetPixel(newIdx)<=0)
                                 continue;
 
                             // generate signal for each fiber compartment
                             for (unsigned int k=0; k<m_FiberModels.size(); k++)
                             {
                                 DoubleDwiType::Pointer doubleDwi = compartments.at(k);
                                 m_FiberModels[k]->SetFiberDirection(dir);
                                 DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx);
                                 pix[g] += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement(g);
                                 doubleDwi->SetPixel(newIdx, pix );
 
                                 double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume;
                                 intraAxonalVolume->SetPixel(idx, vol );
 
                                 if (g==0 && vol>maxVolume)
                                     maxVolume = vol;
                             }
                         }
                     }
                 }
             }
             ++disp;
             unsigned long newTick = 50*disp.count()/disp.expected_count();
             for (int tick = 0; tick<(newTick-lastTick); tick++)
                 m_StatusText += "*";
             lastTick = newTick;
         }
 
         // generate non-fiber signal
         ImageRegionIterator<ItkUcharImgType> it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion());
         double fact = 1;
         if (m_FiberRadius<0.0001)
             fact = voxelVolume/maxVolume;
         while(!it3.IsAtEnd())
         {
             if (it3.Get()>0)
             {
                 DoubleDwiType::IndexType index = it3.GetIndex();
 
                 // get fiber volume fraction
                 DoubleDwiType::Pointer fiberDwi = compartments.at(0);
                 DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment
                 if (fact>1) // auto scale intra-axonal if no fiber radius is specified
                 {
                     fiberPix[g] *= fact;
                     fiberDwi->SetPixel(index, fiberPix);
                 }
                 double f = intraAxonalVolume->GetPixel(index)*fact;
 
                 if (f>voxelVolume || (f>0.0 && m_EnforcePureFiberVoxels) )  // more fiber than space in voxel?
                 {
                     fiberPix[g] *= voxelVolume/f;
                     fiberDwi->SetPixel(index, fiberPix);
                     m_VolumeFractions.at(0)->SetPixel(index, 1);
                 }
                 else
                 {
                     m_VolumeFractions.at(0)->SetPixel(index, f/voxelVolume);
 
                     double nonf = voxelVolume-f;    // non-fiber volume
                     double inter = 0;
                     if (m_FiberModels.size()>1)
                         inter = nonf * f/voxelVolume;   // inter-axonal fraction of non fiber compartment scales linearly with f
                     double other = nonf - inter;        // rest of compartment
                     double singleinter = inter/(m_FiberModels.size()-1);
 
                     // adjust non-fiber and intra-axonal signal
                     for (unsigned int i=1; i<m_FiberModels.size(); i++)
                     {
                         DoubleDwiType::Pointer doubleDwi = compartments.at(i);
                         DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
                         if (f>0)
                             pix[g] /= f;
                         pix[g] *= singleinter;
                         doubleDwi->SetPixel(index, pix);
                         m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume);
                     }
                     for (unsigned int i=0; i<m_NonFiberModels.size(); i++)
                     {
                         DoubleDwiType::Pointer doubleDwi = compartments.at(i+m_FiberModels.size());
                         DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
                         //                        if (dynamic_cast< mitk::AstroStickModel<double>* >(m_NonFiberModels.at(i)))
                         //                        {
                         //                            mitk::AstroStickModel<double>* model = dynamic_cast< mitk::AstroStickModel<double>* >(m_NonFiberModels.at(i));
                         //                            model->SetSeed(8111984);
                         //                        }
                         pix[g] += m_NonFiberModels[i]->SimulateMeasurement(g)*other*m_NonFiberModels[i]->GetWeight();
                         doubleDwi->SetPixel(index, pix);
                         m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight());
                     }
                 }
             }
             ++it3;
         }
 
         // move fibers
         if (m_AddMotionArtifact)
         {
             if (m_RandomMotion)
             {
                 fiberBundleTransformed = fiberBundle->GetDeepCopy();
                 rotation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[0]*2)-m_MaxRotation[0];
                 rotation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[1]*2)-m_MaxRotation[1];
                 rotation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[2]*2)-m_MaxRotation[2];
                 translation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[0]*2)-m_MaxTranslation[0];
                 translation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[1]*2)-m_MaxTranslation[1];
                 translation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[2]*2)-m_MaxTranslation[2];
             }
 
             // rotate mask image
             if (maskImageSet)
             {
                 ImageRegionIterator<ItkUcharImgType> maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion());
                 tempTissueMask->FillBuffer(0);
 
                 while(!maskIt.IsAtEnd())
                 {
                     if (maskIt.Get()<=0)
                     {
                         ++maskIt;
                         continue;
                     }
 
                     DoubleDwiType::IndexType index = maskIt.GetIndex();
                     itk::Point<double, 3> point;
                     upsampledTissueMask->TransformIndexToPhysicalPoint(index, point);
                     if (m_RandomMotion)
                         point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]);
                     else
                         point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1));
 
                     tempTissueMask->TransformPhysicalPointToIndex(point, index);
                     if (tempTissueMask->GetLargestPossibleRegion().IsInside(index))
                         tempTissueMask->SetPixel(index,100);
                     ++maskIt;
                 }
             }
 
             // rotate fibers
             logFile << g+1 << " rotation:" << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";";
             logFile << " translation:" << translation[0] << "," << translation[1] << "," << translation[2] << "\n";
             fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]);
         }
     }
     logFile.close();
     m_StatusText += "\n\n";
     if (this->GetAbortGenerateData())
     {
         m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
         return;
     }
 
     // do k-space stuff
     DoubleDwiType::Pointer doubleOutImage;
     if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents || m_AddGibbsRinging || m_Wrap<1.0)
     {
         m_StatusText += this->GetTime()+" > Adjusting complex signal\n";
         MITK_INFO << "Adjusting complex signal:";
 
         if (m_SimulateRelaxation)
             m_StatusText += "Simulating signal relaxation\n";
         if (m_FrequencyMap.IsNotNull())
             m_StatusText += "Simulating distortions\n";
         if (m_AddGibbsRinging)
             m_StatusText += "Simulating ringing artifacts\n";
         if (m_SimulateEddyCurrents)
             m_StatusText += "Simulating eddy currents\n";
         if (m_Spikes>0)
             m_StatusText += "Simulating spikes\n";
         if (m_Wrap<1.0)
             m_StatusText += "Simulating aliasing artifacts\n";
         if (m_kOffset>0)
             m_StatusText += "Simulating ghosts\n";
 
         doubleOutImage = DoKspaceStuff(compartments);
         m_SignalScale = 1;
     }
     else
     {
         m_StatusText += this->GetTime()+" > Summing compartments\n";
         MITK_INFO << "Summing compartments";
         doubleOutImage = compartments.at(0);
 
         for (unsigned int i=1; i<compartments.size(); i++)
         {
             itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New();
             adder->SetInput1(doubleOutImage);
             adder->SetInput2(compartments.at(i));
             adder->Update();
             doubleOutImage = adder->GetOutput();
         }
     }
     if (this->GetAbortGenerateData())
     {
         m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
         return;
     }
 
     m_StatusText += this->GetTime()+" > Finalizing image\n";
     MITK_INFO << "Finalizing image";
     if (m_SignalScale>1)
         m_StatusText += " Scaling signal\n";
     if (m_NoiseModel!=NULL)
         m_StatusText += " Adding noise\n";
     unsigned int window = 0;
     unsigned int min = itk::NumericTraits<unsigned int>::max();
     ImageRegionIterator<OutputImageType> it4 (outImage, outImage->GetLargestPossibleRegion());
     DoubleDwiType::PixelType signal; signal.SetSize(m_FiberModels[0]->GetNumGradients());
     boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels());
 
     m_StatusText += "0%   10   20   30   40   50   60   70   80   90   100%\n";
     m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
     lastTick = 0;
 
     while(!it4.IsAtEnd())
     {
         if (this->GetAbortGenerateData())
         {
             m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
             return;
         }
 
         ++disp2;
         unsigned long newTick = 50*disp2.count()/disp2.expected_count();
         for (int tick = 0; tick<(newTick-lastTick); tick++)
             m_StatusText += "*";
         lastTick = newTick;
 
         typename OutputImageType::IndexType index = it4.GetIndex();
         signal = doubleOutImage->GetPixel(index)*m_SignalScale;
 
         if (m_NoiseModel!=NULL)
         {
             DoubleDwiType::PixelType accu = signal; accu.Fill(0.0);
             for (unsigned int i=0; i<m_NumberOfRepetitions; i++)
             {
                 DoubleDwiType::PixelType temp = signal;
                 m_NoiseModel->AddNoise(temp);
                 accu += temp;
             }
             signal = accu/m_NumberOfRepetitions;
         }
 
         for (unsigned int i=0; i<signal.Size(); i++)
         {
             if (signal[i]>0)
                 signal[i] = floor(signal[i]+0.5);
             else
                 signal[i] = ceil(signal[i]-0.5);
 
             if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]>window)
                 window = signal[i];
             if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]<min)
                 min = signal[i];
         }
         it4.Set(signal);
         ++it4;
     }
     window -= min;
     unsigned int level = window/2 + min;
     m_LevelWindow.SetLevelWindow(level, window);
     this->SetNthOutput(0, outImage);
 
     m_StatusText += "\n\n";
     m_StatusText += "Finished simulation\n";
     m_StatusText += "Simulation time: "+GetTime();
 }
 
 template< class PixelType >
 itk::Point<float, 3> TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3])
 {
     itk::Point<float, 3> itkPoint;
     itkPoint[0] = point[0];
     itkPoint[1] = point[1];
     itkPoint[2] = point[2];
     return itkPoint;
 }
 
 template< class PixelType >
 itk::Vector<double, 3> TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3])
 {
     itk::Vector<double, 3> itkVector;
     itkVector[0] = point[0];
     itkVector[1] = point[1];
     itkVector[2] = point[2];
     return itkVector;
 }
 
 template< class PixelType >
 vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3])
 {
     vnl_vector_fixed<double, 3> vnlVector;
     vnlVector[0] = point[0];
     vnlVector[1] = point[1];
     vnlVector[2] = point[2];
     return vnlVector;
 }
 
 template< class PixelType >
 vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector<float,3>& vector)
 {
     vnl_vector_fixed<double, 3> vnlVector;
     vnlVector[0] = vector[0];
     vnlVector[1] = vector[1];
     vnlVector[2] = vector[2];
     return vnlVector;
 }
 
 template< class PixelType >
 std::string TractsToDWIImageFilter< PixelType >::GetTime()
 {
     unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC;
     unsigned long hours = total/3600;
     unsigned long minutes = (total%3600)/60;
     unsigned long seconds = total%60;
     std::string out = "";
     out.append(boost::lexical_cast<std::string>(hours));
     out.append(":");
     out.append(boost::lexical_cast<std::string>(minutes));
     out.append(":");
     out.append(boost::lexical_cast<std::string>(seconds));
     return out;
 }
 
 }