diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp index d95ebc8bae..ee1c3d3df1 100644 --- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp @@ -1,497 +1,497 @@ /*=================================================================== 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 //#endif #include #include #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #include #include #include #include namespace itk { template< class ScalarType > KspaceImageFilter< ScalarType >::KspaceImageFilter() : m_Z(0) , m_RandSeed(-1) , m_SpikesPerSlice(0) , m_IsBaseline(true) { m_DiffusionGradientDirection.Fill(0.0); m_CoilPosition.Fill(0.0); } template< class ScalarType > void KspaceImageFilter< ScalarType > ::BeforeThreadedGenerateData() { m_Spike = vcl_complex(0,0); m_SpikeLog = ""; m_TransX = -m_Translation[0]; m_TransY = -m_Translation[1]; m_TransZ = -m_Translation[2]; kxMax = m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(0); kyMax = m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(1); xMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); // scanner coverage in x-direction yMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); // scanner coverage in y-direction yMaxFov = yMax; if (m_Parameters->m_Misc.m_DoAddAliasing) { // actual FOV in y-direction (in x-direction FOV=xMax) yMaxFov = static_cast(yMaxFov * m_Parameters->m_SignalGen.m_CroppingFactor); } yMaxFov_half = (yMaxFov-1)/2; numPix = kxMax*kyMax; float ringing_factor = static_cast(m_Parameters->m_SignalGen.m_ZeroRinging)/100.0; ringing_lines_x = static_cast(ceil(kxMax/2 * ringing_factor)); ringing_lines_y = static_cast(ceil(kyMax/2 * ringing_factor)); // Adjust noise variance since it is the intended variance in physical space and not in k-space: float noiseVar = m_Parameters->m_SignalGen.m_PartialFourier*m_Parameters->m_SignalGen.m_NoiseVariance/(kyMax*kxMax); m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); if (m_RandSeed>=0) // always generate the same random numbers? m_RandGen->SetSeed(m_RandSeed); else m_RandGen->SetSeed(); typename OutputImageType::Pointer outputImage = OutputImageType::New(); itk::ImageRegion<2> region; region.SetSize(0, m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(0)); region.SetSize(1, m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(1)); outputImage->SetLargestPossibleRegion( region ); outputImage->SetBufferedRegion( region ); outputImage->SetRequestedRegion( region ); outputImage->Allocate(); vcl_complex zero = vcl_complex(0, 0); outputImage->FillBuffer(zero); if (m_Parameters->m_SignalGen.m_NoiseVariance>0 && m_Parameters->m_Misc.m_DoAddNoise) { ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion()); while( !oit.IsAtEnd() ) { oit.Set(vcl_complex(m_RandGen->GetNormalVariate(0, noiseVar), m_RandGen->GetNormalVariate(0, noiseVar))); ++oit; } } m_KSpaceImage = InputImageType::New(); m_KSpaceImage->SetLargestPossibleRegion( region ); m_KSpaceImage->SetBufferedRegion( region ); m_KSpaceImage->SetRequestedRegion( region ); m_KSpaceImage->Allocate(); m_KSpaceImage->FillBuffer(0.0); - m_TickImage = InputImageType::New(); - m_TickImage->SetLargestPossibleRegion( region ); - m_TickImage->SetBufferedRegion( region ); - m_TickImage->SetRequestedRegion( region ); - m_TickImage->Allocate(); - m_TickImage->FillBuffer(-1.0); +// m_TickImage = InputImageType::New(); +// m_TickImage->SetLargestPossibleRegion( region ); +// m_TickImage->SetBufferedRegion( region ); +// m_TickImage->SetRequestedRegion( region ); +// m_TickImage->Allocate(); +// m_TickImage->FillBuffer(-1.0); m_Gamma = 42576000*itk::Math::twopi; // Gyromagnetic ratio in Hz/T (1.5T) if ( m_Parameters->m_SignalGen.m_EddyStrength>0 && m_DiffusionGradientDirection.GetNorm()>0.001) { m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_Parameters->m_SignalGen.m_EddyStrength/1000 * m_Gamma; m_IsBaseline = false; } else { m_IsBaseline = true; } this->SetNthOutput(0, outputImage); for (int i=0; i<3; i++) for (int j=0; j<3; j++) m_Transform[i][j] = m_Parameters->m_SignalGen.m_ImageDirection[i][j] * m_Parameters->m_SignalGen.m_ImageSpacing[j]/1000; float a = m_Parameters->m_SignalGen.m_ImageRegion.GetSize(0)*m_Parameters->m_SignalGen.m_ImageSpacing[0]; float b = m_Parameters->m_SignalGen.m_ImageRegion.GetSize(1)*m_Parameters->m_SignalGen.m_ImageSpacing[1]; float diagonal = sqrt(a*a+b*b)/1000; // image diagonal in m switch (m_Parameters->m_SignalGen.m_CoilSensitivityProfile) { case SignalGenerationParameters::COIL_CONSTANT: { m_CoilSensitivityFactor = 1; // same signal everywhere break; } case SignalGenerationParameters::COIL_LINEAR: { m_CoilSensitivityFactor = -1/diagonal; // about 50% of the signal in the image center remaining break; } case SignalGenerationParameters::COIL_EXPONENTIAL: { m_CoilSensitivityFactor = -log(0.1)/diagonal; // about 32% of the signal in the image center remaining break; } } switch (m_Parameters->m_SignalGen.m_AcquisitionType) { case SignalGenerationParameters::SingleShotEpi: m_ReadoutScheme = new mitk::SingleShotEpi(m_Parameters); break; case SignalGenerationParameters::ConventionalSpinEcho: m_ReadoutScheme = new mitk::ConventionalSpinEcho(m_Parameters); break; case SignalGenerationParameters::FastSpinEcho: m_ReadoutScheme = new mitk::FastSpinEcho(m_Parameters); break; default: m_ReadoutScheme = new mitk::SingleShotEpi(m_Parameters); } m_ReadoutScheme->AdjustEchoTime(); m_MovedFmap = nullptr; if (m_Parameters->m_Misc.m_DoAddDistortions && m_Parameters->m_SignalGen.m_FrequencyMap.IsNotNull() && m_Parameters->m_SignalGen.m_DoAddMotion) { // we have to account for the head motion since this also moves our frequency map itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::Pointer fmapInterpolator; fmapInterpolator = itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::New(); fmapInterpolator->SetInputImage(m_Parameters->m_SignalGen.m_FrequencyMap); m_MovedFmap = itk::Image< ScalarType, 2 >::New(); m_MovedFmap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_MovedFmap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_MovedFmap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_MovedFmap->Allocate(); m_MovedFmap->FillBuffer(0); ImageRegionIterator< InputImageType > it(m_MovedFmap, m_MovedFmap->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { itk::Image::IndexType index; index[0] = it.GetIndex()[0]; index[1] = it.GetIndex()[1]; index[2] = m_Zidx; itk::Point point3D; m_Parameters->m_SignalGen.m_FrequencyMap->TransformIndexToPhysicalPoint(index, point3D); m_FiberBundle->TransformPoint( point3D, m_RotationMatrix, m_TransX, m_TransY, m_TransZ ); it.Set(mitk::imv::GetImageValue(point3D, true, fmapInterpolator)); ++it; } } // calculate T1 relaxation (independent of actual readout) m_T1Relax.clear(); if ( m_Parameters->m_SignalGen.m_DoSimulateRelaxation) for (unsigned int i=0; im_SignalGen.m_tRep/m_T1[i])); // account for inversion pulse and TI if (m_Parameters->m_SignalGen.m_tInv > 0) relaxation *= (1.0-std::exp(std::log(2) - m_Parameters->m_SignalGen.m_tInv/m_T1[i])); m_T1Relax.push_back(relaxation); } } template< class ScalarType > float KspaceImageFilter< ScalarType >::CoilSensitivity(VectorType& pos) { // ************************************************************************* // Coil ring is moving with excited slice (FIX THIS SOMETIME) m_CoilPosition[2] = pos[2]; // ************************************************************************* switch (m_Parameters->m_SignalGen.m_CoilSensitivityProfile) { case SignalGenerationParameters::COIL_CONSTANT: return 1; case SignalGenerationParameters::COIL_LINEAR: { VectorType diff = pos-m_CoilPosition; float sens = diff.GetNorm()*m_CoilSensitivityFactor + 1; if (sens<0) sens = 0; return sens; } case SignalGenerationParameters::COIL_EXPONENTIAL: { VectorType diff = pos-m_CoilPosition; float dist = static_cast(diff.GetNorm()); return std::exp(-dist*m_CoilSensitivityFactor); } default: return 1; } } template< class ScalarType > void KspaceImageFilter< ScalarType > ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType ) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; // precalculate shifts for DFT float x_shift = 0; float y_shift = 0; if (static_cast(xMax)%2==1) x_shift = (xMax-1)/2; else x_shift = xMax/2; if (static_cast(yMax)%2==1) y_shift = (yMax-1)/2; else y_shift = yMax/2; float kx_shift = 0; float ky_shift = 0; if (static_cast(kxMax)%2==1) kx_shift = (kxMax-1)/2; else kx_shift = kxMax/2; if (static_cast(kyMax)%2==1) ky_shift = (kyMax-1)/2; else ky_shift = kyMax/2; vcl_complex zero = vcl_complex(0, 0); while( !oit.IsAtEnd() ) { int tick = oit.GetIndex()[1] * kxMax + oit.GetIndex()[0]; // get current k-space index (depends on the chosen k-space readout scheme) itk::Index< 2 > kIdx = m_ReadoutScheme->GetActualKspaceIndex(tick); // we have to adjust the ticks to obtain correct times since the DFT is not completely symmetric in the even number of lines case if (static_cast(kyMax)%2 == 0 && !m_Parameters->m_SignalGen.m_ReversePhase) { tick += kxMax; tick %= static_cast(numPix); } // partial fourier // two cases because we always want to skip the "later" parts of k-space // in "normal" phase direction, the higher k-space indices are acquired first // in reversed phase direction, the higher k-space indices are acquired later // if the image has an even number of lines, never skip line zero since it is missing on the other side (DFT not completely syymetric in even case) if ((m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]>std::ceil(kyMax*m_Parameters->m_SignalGen.m_PartialFourier)) || (!m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]m_SignalGen.m_PartialFourier)) && (kIdx[1]>0 || static_cast(kyMax)%2 == 1))) { outputImage->SetPixel(kIdx, zero); ++oit; continue; } - m_TickImage->SetPixel(kIdx, tick); +// m_TickImage->SetPixel(kIdx, tick); // gibbs ringing by setting high frequencies to zero (alternative to using smaller k-space than input image space) if (m_Parameters->m_SignalGen.m_DoAddGibbsRinging && m_Parameters->m_SignalGen.m_ZeroRinging>0) { if (kIdx[0] < ringing_lines_x || kIdx[1] < ringing_lines_y || kIdx[0] >= kxMax - ringing_lines_x || kIdx[1] >= kyMax - ringing_lines_y) { outputImage->SetPixel(kIdx, zero); ++oit; continue; } } // time passes since application of the RF pulse float tRf = m_ReadoutScheme->GetTimeFromRf(tick); // calculate eddy current decay factor float eddyDecay = 0; if ( m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline) { // time passed since k-space readout started float tRead = m_ReadoutScheme->GetTimeFromLastDiffusionGradient(tick); eddyDecay = std::exp(-tRead/m_Parameters->m_SignalGen.m_Tau ) * tRead/1000; // time in seconds here } // calcualte signal relaxation factors std::vector< float > relaxFactor; if ( m_Parameters->m_SignalGen.m_DoSimulateRelaxation) { // time from maximum echo float t = m_ReadoutScheme->GetTimeFromMaxEcho(tick); for (unsigned int i=0; im_SignalGen.m_tInhom)); } } // shift k for DFT: (0 -- N) --> (-N/2 -- N/2) float kx = kIdx[0] - kx_shift; float ky = kIdx[1] - ky_shift; // add ghosting by adding gradient delay induced offset if (m_Parameters->m_Misc.m_DoAddGhosts) { if (kIdx[1]%2 == 1) kx -= m_Parameters->m_SignalGen.m_KspaceLineOffset; else kx += m_Parameters->m_SignalGen.m_KspaceLineOffset; } // pull stuff out of inner loop tRf /= 1000; // time in seconds kx /= xMax; ky /= yMaxFov; // calculate signal s at k-space position (kx, ky) vcl_complex s(0,0); InputIteratorType it(m_CompartmentImages[0], m_CompartmentImages[0]->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { typename InputImageType::IndexType input_idx = it.GetIndex(); // shift x,y for DFT: (0 -- N) --> (-N/2 -- N/2) float x = input_idx[0] - x_shift; float y = input_idx[1] - y_shift; // sum compartment signals and simulate relaxation ScalarType f_real = 0; for (unsigned int i=0; im_SignalGen.m_DoSimulateRelaxation) f_real += m_CompartmentImages[i]->GetPixel(input_idx) * relaxFactor[i]; else f_real += m_CompartmentImages[i]->GetPixel(input_idx); // vector from image center to current position (in meter) // only necessary for eddy currents and non-constant coil sensitivity VectorType pos; if ((m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline) || m_Parameters->m_SignalGen.m_CoilSensitivityProfile!=SignalGenerationParameters::COIL_CONSTANT) { pos[0] = x; pos[1] = y; pos[2] = m_Z; pos = m_Transform*pos; } if (m_Parameters->m_SignalGen.m_CoilSensitivityProfile!=SignalGenerationParameters::COIL_CONSTANT) f_real *= CoilSensitivity(pos); // simulate eddy currents and other distortions float omega = 0; // frequency offset if ( m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline) { // duration (tRead) already included in "eddyDecay" omega += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2]) * eddyDecay; } // simulate distortions if (m_Parameters->m_Misc.m_DoAddDistortions) { if (m_MovedFmap.IsNotNull()) // if we have headmotion, use moved map omega += m_MovedFmap->GetPixel(input_idx) * tRf; else if (m_Parameters->m_SignalGen.m_FrequencyMap.IsNotNull()) { itk::Image::IndexType index; index[0] = input_idx[0]; index[1] = input_idx[1]; index[2] = m_Zidx; omega += m_Parameters->m_SignalGen.m_FrequencyMap->GetPixel(index) * tRf; } } // if signal comes from outside FOV, mirror it back (wrap-around artifact - aliasing if (m_Parameters->m_Misc.m_DoAddAliasing) { if (y<-yMaxFov_half) y += yMaxFov; else if (y>yMaxFov_half) y -= yMaxFov; } // actual DFT term vcl_complex f(f_real * m_Parameters->m_SignalGen.m_SignalScale, 0); s += f * std::exp( std::complex(0, itk::Math::twopi * (kx*x + ky*y + omega )) ); ++it; } s /= numPix; if (m_SpikesPerSlice>0 && sqrt(s.imag()*s.imag()+s.real()*s.real()) > sqrt(m_Spike.imag()*m_Spike.imag()+m_Spike.real()*m_Spike.real()) ) m_Spike = s; s += outputImage->GetPixel(kIdx); // add precalculated noise outputImage->SetPixel(kIdx, s); m_KSpaceImage->SetPixel(kIdx, sqrt(s.imag()*s.imag()+s.real()*s.real()) ); ++oit; } } template< class ScalarType > void KspaceImageFilter< ScalarType > ::AfterThreadedGenerateData() { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); int kxMax = outputImage->GetLargestPossibleRegion().GetSize(0); // k-space size in x-direction int kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); // k-space size in y-direction ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion()); while( !oit.IsAtEnd() ) // use hermitian k-space symmetry to fill empty k-space parts resulting from partial fourier acquisition { int tick = oit.GetIndex()[1] * kxMax + oit.GetIndex()[0]; auto kIdx = m_ReadoutScheme->GetActualKspaceIndex(tick); if ((m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]>std::ceil(kyMax*m_Parameters->m_SignalGen.m_PartialFourier)) || (!m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]m_SignalGen.m_PartialFourier)) && (kIdx[1]>0 || static_cast(kyMax)%2 == 1))) { // calculate symmetric index auto sym = m_ReadoutScheme->GetSymmetricIndex(kIdx); // use complex conjugate of symmetric index value at current index vcl_complex s = outputImage->GetPixel(sym); s = vcl_complex(s.real(), -s.imag()); outputImage->SetPixel(kIdx, s); m_KSpaceImage->SetPixel(kIdx, sqrt(s.imag()*s.imag()+s.real()*s.real()) ); } ++oit; } m_Spike *= m_Parameters->m_SignalGen.m_SpikeAmplitude; itk::Index< 2 > spikeIdx; for (unsigned int i=0; iGetIntegerVariate()%kxMax; spikeIdx[1] = m_RandGen->GetIntegerVariate()%kyMax; outputImage->SetPixel(spikeIdx, m_Spike); m_SpikeLog += "[" + boost::lexical_cast(spikeIdx[0]) + "," + boost::lexical_cast(spikeIdx[1]) + "," + boost::lexical_cast(m_Zidx) + "] Magnitude: " + boost::lexical_cast(m_Spike.real()) + "+" + boost::lexical_cast(m_Spike.imag()) + "i\n"; } delete m_ReadoutScheme; - typename itk::ImageFileWriter< InputImageType >::Pointer wr = itk::ImageFileWriter< InputImageType >::New(); - wr->SetInput(m_TickImage); - wr->SetFileName("/home/neher/TimeFromRfImage.nii.gz"); - wr->Update(); +// typename itk::ImageFileWriter< InputImageType >::Pointer wr = itk::ImageFileWriter< InputImageType >::New(); +// wr->SetInput(m_TickImage); +// wr->SetFileName("/home/neher/TimeFromRfImage.nii.gz"); +// wr->Update(); } } #endif