diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.cpp index 7d1e74bb7b..cd9c9b6599 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.cpp @@ -1,80 +1,90 @@ /*=================================================================== 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 __itkDftImageFilter_txx #define __itkDftImageFilter_txx #include #include #include #include "itkDftImageFilter.h" #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > DftImageFilter< TPixelType > ::DftImageFilter() { this->SetNumberOfRequiredInputs( 1 ); } template< class TPixelType > void DftImageFilter< 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; typename InputImageType::Pointer inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); int szx = outputImage->GetLargestPossibleRegion().GetSize(0); int szy = outputImage->GetLargestPossibleRegion().GetSize(1); while( !oit.IsAtEnd() ) { int kx = oit.GetIndex()[0]; int ky = oit.GetIndex()[1]; + if( kx < szx/2 ) + kx = kx + szx/2; + else + kx = kx - szx/2; + + if( ky < szy/2 ) + ky = ky + szy/2; + else + ky = ky - szy/2; + vcl_complex s(0,0); InputIteratorType it(inputImage, inputImage->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { int x = it.GetIndex()[0]; int y = it.GetIndex()[1]; vcl_complex f(it.Get().real(), it.Get().imag()); s += f * exp( std::complex(0, -2 * M_PI * (kx*(double)x/szx + ky*(double)y/szy) ) ); ++it; } double magn = sqrt(s.real()*s.real()+s.imag()*s.imag()); oit.Set(magn); ++oit; } } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.h index ee2235cee4..0eb66c2669 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkDftImageFilter.h @@ -1,74 +1,74 @@ /*=================================================================== 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. ===================================================================*/ /*=================================================================== This file is based heavily on a corresponding ITK filter. ===================================================================*/ #ifndef __itkDftImageFilter_h_ #define __itkDftImageFilter_h_ #include "FiberTrackingExports.h" #include #include #include namespace itk{ /** -* \brief 2D Discrete Fourier Transform Filter (complex to real) */ +* \brief 2D Discrete Fourier Transform Filter (complex to real). Special issue for Fiberfox -> rearranges slice. */ template< class TPixelType > class DftImageFilter : public ImageToImageFilter< Image< vcl_complex< TPixelType > >, Image< TPixelType > > { public: typedef DftImageFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< Image< vcl_complex< TPixelType > >, Image< TPixelType > > Superclass; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(DftImageFilter, ImageToImageFilter) typedef typename Superclass::InputImageType InputImageType; typedef typename Superclass::OutputImageType OutputImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; protected: DftImageFilter(); ~DftImageFilter() {} void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId); private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkDftImageFilter.cpp" #endif #endif //__itkDftImageFilter_h_ diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp index 8e17833eb6..0e4aa5191b 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp @@ -1,245 +1,238 @@ /*=================================================================== 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 #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #define _USE_MATH_DEFINES #include 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_DiffusionGradientDirection.Fill(0.0); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::BeforeThreadedGenerateData() { typename OutputImageType::Pointer outputImage = OutputImageType::New(); outputImage->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); outputImage->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); outputImage->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); 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->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_TEMPIMAGE->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_TEMPIMAGE->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); 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->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_FrequencyMap->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_FrequencyMap->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); 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_DiffusionGradientDirection.Normalize(); m_EddyGradientMagnitude /= 1000; // eddy gradient magnitude in T/m + m_DiffusionGradientDirection.Normalize(); m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_EddyGradientMagnitude * gamma; m_IsBaseline = false; } - else - m_EddyGradientMagnitude = gamma*m_EddyGradientMagnitude/1000; 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); double kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); double numPix = kxMax*kyMax; double dt = m_tLine/kxMax; double fromMaxEcho = - m_tLine*kyMax/2; double in_szx = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); double in_szy = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); int xOffset = in_szx-kxMax; int yOffset = in_szy-kyMax; vcl_complex 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 (int i=0; i=kxMax/2) kx += xOffset; if (ky>=kyMax/2) ky += yOffset; vcl_complex s(0,0); InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { - double x = it.GetIndex()[0]; - double y = it.GetIndex()[1]; + double x = it.GetIndex()[0]-in_szx/2; + double y = it.GetIndex()[1]-in_szy/2; vcl_complex f(0, 0); // sum compartment signals and simulate relaxation for (int i=0; i( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_SignalScale, 0); else f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_SignalScale ); // simulate eddy currents and other distortions double omega_t = 0; - if ( m_SimulateEddyCurrents ) + if ( m_SimulateEddyCurrents && !m_IsBaseline) { - if (!m_IsBaseline) - { - itk::Vector< double, 3 > pos; pos[0] = x-kxMax/2; pos[1] = y-kyMax/2; 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; - } - else - omega_t += m_EddyGradientMagnitude*eddyDecay; + 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; // actual DFT term s += f * exp( std::complex(0, 2 * M_PI * (kx*x/in_szx + ky*y/in_szy + 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())); + // 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 spikeIdx; spikeIdx[0] = rand()%(int)kxMax; spikeIdx[1] = rand()%(int)kyMax; 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(); + // 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/itkKspaceImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h index 86a57496ba..f5e99c93ef 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h @@ -1,122 +1,123 @@ /*=================================================================== 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. ===================================================================*/ /*=================================================================== This file is based heavily on a corresponding ITK filter. ===================================================================*/ #ifndef __itkKspaceImageFilter_h_ #define __itkKspaceImageFilter_h_ #include "FiberTrackingExports.h" #include #include #include namespace itk{ /** * \brief Performes deterministic streamline tracking on the input tensor image. */ template< class TPixelType > class KspaceImageFilter : public ImageSource< Image< vcl_complex< TPixelType >, 2 > > { public: typedef KspaceImageFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageSource< Image< vcl_complex< TPixelType >, 2 > > Superclass; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(KspaceImageFilter, ImageToImageFilter) typedef typename itk::Image< double, 2 > InputImageType; typedef typename InputImageType::Pointer InputImagePointerType; typedef typename Superclass::OutputImageType OutputImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; typedef itk::Matrix MatrixType; + typedef itk::Point Point2D; itkSetMacro( FrequencyMap, typename InputImageType::Pointer ) itkSetMacro( tLine, double ) itkSetMacro( kOffset, double ) itkSetMacro( TE, double) itkSetMacro( Tinhom, double) itkSetMacro( Tau, double) itkSetMacro( SimulateRelaxation, bool ) itkSetMacro( SimulateEddyCurrents, bool ) itkSetMacro( Z, double ) itkSetMacro( DirectionMatrix, MatrixType ) itkSetMacro( SignalScale, double ) itkSetMacro( OutSize, itk::Size<2> ) itkSetMacro( Spikes, int ) itkSetMacro( SpikeAmplitude, double ) void SetT2( std::vector< double > t2Vector ) { m_T2=t2Vector; } void SetCompartmentImages( std::vector< InputImagePointerType > cImgs ) { m_CompartmentImages=cImgs; } void SetDiffusionGradientDirection(itk::Vector g) { m_DiffusionGradientDirection=g; } void SetEddyGradientMagnitude(double g_mag) { m_EddyGradientMagnitude=g_mag; } ///< in T/m protected: KspaceImageFilter(); ~KspaceImageFilter() {} void BeforeThreadedGenerateData(); void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId); void AfterThreadedGenerateData(); bool m_SimulateRelaxation; bool m_SimulateDistortions; bool m_SimulateEddyCurrents; typename InputImageType::Pointer m_TEMPIMAGE; typename InputImageType::Pointer m_FrequencyMap; double m_tLine; double m_kOffset; double m_Tinhom; double m_TE; std::vector< double > m_T2; std::vector< InputImagePointerType > m_CompartmentImages; itk::Vector m_DiffusionGradientDirection; double m_Tau; ///< eddy current decay constant double m_EddyGradientMagnitude; ///< in T/m double m_Z; MatrixType m_DirectionMatrix; bool m_IsBaseline; double m_SignalScale; itk::Size<2> m_OutSize; int m_Spikes; double m_SpikeAmplitude; private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkKspaceImageFilter.cpp" #endif #endif //__itkKspaceImageFilter_h_ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index 2475fd4b65..b731249686 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2453 +1,2453 @@ QmitkFiberfoxViewControls 0 0 435 1764 Form Save Parameters 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid Operations false Join Bundles QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles false Transform Selection If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Data Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Image Settings QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 TE in milliseconds 1 10000 1 100 Interpolation Shrink: Line Readout Time: false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html> 0 10000 0 Signal Scale: color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 1 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options Qt::Vertical 20 40 Noise and other Artifacts Add Spikes false Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 - 0.100000000000000 + 0.250000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of Rician noise model. 4 0.000000000000000 100000.000000000000000 0.001000000000000 - 25.000000000000000 + 50.000000000000000 Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Add Rician Noise false Add Distortions false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Upsampling: false Larger values increase the ringing range. Beware of performance issues! 2 1.000000000000000 10.000000000000000 0.100000000000000 2.000000000000000 !!!EXPERIMENTAL!!! Add Eddy Current Effects false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Magnitude: false Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 - 0.001000000000000 + 0.005000000000000 color: rgb(255, 0, 0); Experimental! true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Weighting factor between the two extra-axonal compartments. 1.000000000000000 0.100000000000000 0.300000000000000 Compartment Fraction: true Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. Generate Image Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model Load Parameters QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddDistortions m_FrequencyMapBox m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_ImageUpsamplingBox m_SaveParametersButton m_LoadParametersButton tabWidget