diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index f46691dc1b..1987fdcad1 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,607 +1,612 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { TractsToDWIImageFilter::TractsToDWIImageFilter() : m_CircleDummy(false) , m_VolumeAccuracy(10) , m_Upsampling(1) , m_NumberOfRepetitions(1) , m_EnforcePureFiberVoxels(false) , m_InterpolationShrink(10) , m_FiberRadius(20) , m_SignalScale(300) { 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); } TractsToDWIImageFilter::~TractsToDWIImageFilter() { } std::vector< TractsToDWIImageFilter::DoubleDwiType::Pointer > TractsToDWIImageFilter::AddKspaceArtifacts( std::vector< DoubleDwiType::Pointer >& images ) { // create slice object SliceType::Pointer slice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); slice->SetLargestPossibleRegion( region ); slice->SetBufferedRegion( region ); slice->SetRequestedRegion( region ); slice->Allocate(); boost::progress_display disp(images.size()*images[0]->GetVectorLength()*images[0]->GetLargestPossibleRegion().GetSize(2)); std::vector< DoubleDwiType::Pointer > outImages; for (int i=0; iSetSpacing( m_Spacing ); newImage->SetOrigin( m_Origin ); newImage->SetDirection( m_DirectionMatrix ); newImage->SetLargestPossibleRegion( m_ImageRegion ); newImage->SetBufferedRegion( m_ImageRegion ); newImage->SetRequestedRegion( m_ImageRegion ); newImage->SetVectorLength( image->GetVectorLength() ); newImage->Allocate(); DiffusionSignalModel* signalModel; if (iGetVectorLength(); g++) for (int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { ++disp; // extract slice from channel g for (int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::PixelType pix2D = image->GetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); } // fourier transform slice itk::FFTRealToComplexConjugateImageFilter< SliceType::PixelType, 2 >::Pointer fft = itk::FFTRealToComplexConjugateImageFilter< SliceType::PixelType, 2 >::New(); fft->SetInput(slice); fft->Update(); ComplexSliceType::Pointer fSlice = fft->GetOutput(); fSlice = RearrangeSlice(fSlice); // add artifacts for (int a=0; aSetT2(signalModel->GetT2()); fSlice = m_KspaceArtifacts.at(a)->AddArtifact(fSlice); } // save k-space slice of s0 image if (g==0) for (int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double kpix = sqrt(fSlice->GetPixel(index2D).real()*fSlice->GetPixel(index2D).real()+fSlice->GetPixel(index2D).imag()*fSlice->GetPixel(index2D).imag()); m_KspaceImage->SetPixel(index3D, kpix); } // inverse fourier transform slice SliceType::Pointer newSlice; itk::FFTComplexConjugateToRealImageFilter< SliceType::PixelType, 2 >::Pointer ifft = itk::FFTComplexConjugateToRealImageFilter< SliceType::PixelType, 2 >::New(); ifft->SetInput(fSlice); ifft->Update(); newSlice = ifft->GetOutput(); // put slice back into channel g for (int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } } outImages.push_back(newImage); } return outImages; } TractsToDWIImageFilter::ComplexSliceType::Pointer TractsToDWIImageFilter::RearrangeSlice(ComplexSliceType::Pointer slice) { ImageRegion<2> region = slice->GetLargestPossibleRegion(); ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New(); rearrangedSlice->SetLargestPossibleRegion( region ); rearrangedSlice->SetBufferedRegion( region ); rearrangedSlice->SetRequestedRegion( region ); rearrangedSlice->Allocate(); int xHalf = region.GetSize(0)/2; int yHalf = region.GetSize(1)/2; for (int y=0; y pix = slice->GetPixel(idx); if( idx[0] < xHalf ) idx[0] = idx[0] + xHalf; else idx[0] = idx[0] - xHalf; if( idx[1] < yHalf ) idx[1] = idx[1] + yHalf; else idx[1] = idx[1] - yHalf; rearrangedSlice->SetPixel(idx, pix); } return rearrangedSlice; } void TractsToDWIImageFilter::GenerateData() { // 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_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!"); // determine k-space undersampling for (int i=0; i*>(m_KspaceArtifacts.at(i)) ) m_Upsampling = dynamic_cast*>(m_KspaceArtifacts.at(i))->GetKspaceCropping(); if (m_Upsampling<1) m_Upsampling = 1; if (m_TissueMask.IsNotNull()) { // use input tissue mask m_Spacing = m_TissueMask->GetSpacing(); m_Origin = m_TissueMask->GetOrigin(); m_DirectionMatrix = m_TissueMask->GetDirection(); m_ImageRegion = m_TissueMask->GetLargestPossibleRegion(); if (m_Upsampling>1) { ImageRegion<3> region = m_ImageRegion; region.SetSize(0, m_ImageRegion.GetSize(0)*m_Upsampling); region.SetSize(1, m_ImageRegion.GetSize(1)*m_Upsampling); mitk::Vector3D spacing = m_Spacing; spacing[0] /= m_Upsampling; spacing[1] /= m_Upsampling; itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_TissueMask); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_TissueMask); resampler->SetSize(region.GetSize()); resampler->SetOutputSpacing(spacing); resampler->Update(); m_TissueMask = resampler->GetOutput(); } MITK_INFO << "Using tissue mask"; } // initialize output dwi image OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Spacing ); outImage->SetOrigin( m_Origin ); outImage->SetDirection( m_DirectionMatrix ); outImage->SetLargestPossibleRegion( m_ImageRegion ); outImage->SetBufferedRegion( m_ImageRegion ); outImage->SetRequestedRegion( m_ImageRegion ); outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() ); outImage->Allocate(); OutputImageType::PixelType temp; temp.SetSize(m_FiberModels[0]->GetNumGradients()); temp.Fill(0.0); outImage->FillBuffer(temp); // is input slize size a power of two? int x=2; int y=2; while (x " << x; m_ImageRegion.SetSize(0, x); } if (y!=m_ImageRegion.GetSize(1)) { MITK_INFO << "Adjusting image height: " << m_ImageRegion.GetSize(1) << " --> " << y; m_ImageRegion.SetSize(1, y); } // initialize k-space image m_KspaceImage = ItkDoubleImgType::New(); m_KspaceImage->SetSpacing( m_Spacing ); m_KspaceImage->SetOrigin( m_Origin ); m_KspaceImage->SetDirection( m_DirectionMatrix ); m_KspaceImage->SetLargestPossibleRegion( m_ImageRegion ); m_KspaceImage->SetBufferedRegion( m_ImageRegion ); m_KspaceImage->SetRequestedRegion( m_ImageRegion ); m_KspaceImage->Allocate(); m_KspaceImage->FillBuffer(0); // apply undersampling to image parameters m_UpsampledSpacing = m_Spacing; m_UpsampledImageRegion = m_ImageRegion; m_UpsampledSpacing[0] /= m_Upsampling; m_UpsampledSpacing[1] /= m_Upsampling; m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*m_Upsampling); m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*m_Upsampling); // everything from here on is using the upsampled image parameters!!! if (m_TissueMask.IsNull()) { m_TissueMask = ItkUcharImgType::New(); m_TissueMask->SetSpacing( m_UpsampledSpacing ); m_TissueMask->SetOrigin( m_Origin ); 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); } // resample fiber bundle for sufficient voxel coverage double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy); double mmRadius = m_FiberRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy; // generate double images to wokr with because we don't want to lose precision // we use a separate image for each compartment model std::vector< DoubleDwiType::Pointer > compartments; for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_Origin ); 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); } double interpFact = 2*atan(-0.5*m_InterpolationShrink); double maxVolume = 0; vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments"; boost::progress_display disp(numFibers); for( int i=0; iGetNextCell ( numPoints, points ); if (numPoints<2) continue; for( int j=0; jGetPoint(points[j]); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(points[j+1]))-v; else dir = v-GetItkVector(fiberPolyData->GetPoint(points[j-1])); itk::Index<3> idx; itk::ContinuousIndex contIndex; m_TissueMask->TransformPhysicalPointToIndex(vertex, idx); m_TissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); 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 (!m_TissueMask->GetLargestPossibleRegion().IsInside(newIdx) || m_TissueMask->GetPixel(newIdx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx); pix += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement(); doubleDwi->SetPixel(newIdx, pix ); if (pix[baselineIndex]>maxVolume) maxVolume = pix[baselineIndex]; } } } } } } MITK_INFO << "Generating signal of " << m_NonFiberModels.size() << " non-fiber compartments"; ImageRegionIterator it3(m_TissueMask, m_TissueMask->GetLargestPossibleRegion()); boost::progress_display disp3(m_TissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; double fact = 1; if (m_FiberRadius<0.0001) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { ++disp3; DoubleDwiType::IndexType index = it3.GetIndex(); if (it3.Get()>0) { // 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 *= fact; fiberDwi->SetPixel(index, fiberPix); } double f = fiberPix[baselineIndex]; if (f>voxelVolume || f>0 && m_EnforcePureFiberVoxels) // more fiber than space in voxel? { fiberDwi->SetPixel(index, fiberPix*voxelVolume/f); for (int i=1; iSetPixel(index, pix); } } else { double nonf = voxelVolume-f; // non-fiber volume double inter = 0; if (m_FiberModels.size()>1) inter = nonf * f; // intra-axonal fraction of non fiber compartment scales linearly with f double other = nonf - inter; // rest of compartment // adjust non-fiber and intra-axonal signal for (int i=1; iGetPixel(index); if (pix[baselineIndex]>0) pix /= pix[baselineIndex]; pix *= inter; doubleDwi->SetPixel(index, pix); } for (int i=0; iGetPixel(index) + m_NonFiberModels[i]->SimulateMeasurement()*other*m_NonFiberModels[i]->GetWeight(); doubleDwi->SetPixel(index, pix); } } } ++it3; } // do k-space stuff if (!m_KspaceArtifacts.empty()) MITK_INFO << "Generating k-space artifacts"; else MITK_INFO << "Generating k-space image"; compartments = AddKspaceArtifacts(compartments); MITK_INFO << "Summing compartments and adding noise"; + unsigned int window = 0; ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_FiberModels[0]->GetNumGradients()); boost::progress_display disp4(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); while(!it4.IsAtEnd()) { ++disp4; DWIImageType::IndexType index = it4.GetIndex(); signal.Fill(0.0); // adjust fiber signal for (int i=0; iGetPixel(index)*m_SignalScale; // adjust non-fiber signal for (int i=0; iGetPixel(index)*m_SignalScale; DoubleDwiType::PixelType accu = signal; accu.Fill(0.0); for (int i=0; iAddNoise(temp); accu += temp; } signal = accu/m_NumberOfRepetitions; for (int i=0; i0) 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]; } it4.Set(signal); ++it4; } + unsigned int level = window/2; + m_LevelWindow = mitk::LevelWindow(level, window); this->SetNthOutput(0, outImage); } itk::Point TractsToDWIImageFilter::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } itk::Vector TractsToDWIImageFilter::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } vnl_vector_fixed TractsToDWIImageFilter::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } vnl_vector_fixed TractsToDWIImageFilter::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h index 8708ce140c..b0263fac64 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h @@ -1,130 +1,132 @@ /*=================================================================== 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 __itkTractsToDWIImageFilter_h__ #define __itkTractsToDWIImageFilter_h__ // MITK #include #include #include #include #include #include // ITK #include #include #include #include #include #include typedef itk::VectorImage< short, 3 > DWIImageType; namespace itk { /** * \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. */ class TractsToDWIImageFilter : public ImageSource< DWIImageType > { public: typedef TractsToDWIImageFilter Self; typedef ImageSource< DWIImageType > Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; typedef std::vector< mitk::KspaceArtifact* > KspaceArtifactList; typedef std::vector< mitk::DiffusionSignalModel* > DiffusionModelList; typedef itk::Matrix MatrixType; typedef mitk::DiffusionNoiseModel NoiseModelType; typedef itk::Image< double, 2 > SliceType; typedef itk::FFTRealToComplexConjugateImageFilter< double, 2 >::OutputImageType ComplexSliceType; itkNewMacro(Self) itkTypeMacro( TractsToDWIImageFilter, ImageToImageFilter ) // input itkSetMacro( SignalScale, double ) itkSetMacro( FiberRadius, double ) itkSetMacro( InterpolationShrink, double ) ///< large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation) itkSetMacro( VolumeAccuracy, unsigned int ) ///< determines fiber sampling density and thereby the accuracy of the fiber volume fraction itkSetMacro( FiberBundle, FiberBundleType ) ///< input fiber bundle itkSetMacro( Spacing, mitk::Vector3D ) ///< output image spacing itkSetMacro( Origin, mitk::Point3D ) ///< output image origin itkSetMacro( DirectionMatrix, MatrixType ) ///< output image rotation itkSetMacro( EnforcePureFiberVoxels, bool ) ///< treat all voxels containing at least one fiber as fiber-only (actually disable non-fiber compartments for this voxel). itkSetMacro( ImageRegion, ImageRegion<3> ) ///< output image size itkSetMacro( NumberOfRepetitions, unsigned int ) ///< number of acquisition repetitions to reduce noise (default is no additional repetition) itkSetMacro( TissueMask, ItkUcharImgType::Pointer ) ///< voxels outside of this binary mask contain only noise (are treated as air) itkGetMacro( KspaceImage, ItkDoubleImgType::Pointer ) void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; } ///< generates the noise added to the image values void SetFiberModels(DiffusionModelList modelList){ m_FiberModels = modelList; } ///< generate signal of fiber compartments void SetNonFiberModels(DiffusionModelList modelList){ m_NonFiberModels = modelList; } ///< generate signal of non-fiber compartments void SetKspaceArtifacts(KspaceArtifactList artifactList){ m_KspaceArtifacts = artifactList; } + mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; } void GenerateData(); protected: TractsToDWIImageFilter(); virtual ~TractsToDWIImageFilter(); itk::Point GetItkPoint(double point[3]); itk::Vector GetItkVector(double point[3]); vnl_vector_fixed GetVnlVector(double point[3]); vnl_vector_fixed GetVnlVector(Vector< float, 3 >& vector); /** Transform generated image compartment by compartment, channel by channel and slice by slice using FFT and add k-space artifacts. */ std::vector< DoubleDwiType::Pointer > AddKspaceArtifacts(std::vector< DoubleDwiType::Pointer >& images); /** Rearrange FFT output to shift low frequencies to the iamge center (correct itk). */ TractsToDWIImageFilter::ComplexSliceType::Pointer RearrangeSlice(ComplexSliceType::Pointer slice); mitk::Vector3D m_Spacing; ///< output image spacing mitk::Vector3D m_UpsampledSpacing; mitk::Point3D m_Origin; ///< output image origin MatrixType m_DirectionMatrix; ///< output image rotation ImageRegion<3> m_ImageRegion; ///< output image size ImageRegion<3> m_UpsampledImageRegion; ItkUcharImgType::Pointer m_TissueMask; ///< voxels outside of this binary mask contain only noise (are treated as air) FiberBundleType m_FiberBundle; ///< input fiber bundle DiffusionModelList m_FiberModels; ///< generate signal of fiber compartments DiffusionModelList m_NonFiberModels; ///< generate signal of non-fiber compartments KspaceArtifactList m_KspaceArtifacts; NoiseModelType* m_NoiseModel; ///< generates the noise added to the image values bool m_CircleDummy; unsigned int m_VolumeAccuracy; ItkDoubleImgType::Pointer m_KspaceImage; unsigned int m_Upsampling; unsigned int m_NumberOfRepetitions; bool m_EnforcePureFiberVoxels; double m_InterpolationShrink; double m_FiberRadius; double m_SignalScale; + mitk::LevelWindow m_LevelWindow; }; } #include "itkTractsToDWIImageFilter.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h index aed5503104..a17a7a10f3 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h @@ -1,84 +1,89 @@ /*=================================================================== 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 _MITK_DiffusionSignalModel_H #define _MITK_DiffusionSignalModel_H #include #include #include #include namespace mitk { /** * \brief Abstract class for diffusion signal models * */ template< class ScalarType > class DiffusionSignalModel { public: DiffusionSignalModel() : m_T2(100) , m_Weight(1) {} ~DiffusionSignalModel(){} typedef itk::VariableLengthVector< ScalarType > PixelType; typedef itk::Vector GradientType; typedef std::vector GradientListType; /** Realizes actual signal generation. Has to be implemented in subclass. **/ virtual PixelType SimulateMeasurement() = 0; void SetFiberDirection(GradientType fiberDirection){ m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { m_GradientList = gradientList; } void SetT2(double T2) { m_T2 = T2; } void SetWeight(double Weight) { m_Weight = Weight; } double GetWeight() { return m_Weight; } double GetT2() { return m_T2; } int GetNumGradients(){ return m_GradientList.size(); } std::vector< int > GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientList.size(); i++) if (m_GradientList.at(i).GetNorm()<0.0001) result.push_back(i); return result; } int GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientList.size(); i++) if (m_GradientList.at(i).GetNorm()<0.0001) return i; return -1; } + bool IsBaselineIndex(int idx) + { + if (m_GradientList.size()>idx && m_GradientList.at(idx).GetNorm()>0.0001) + return true; + } protected: GradientType m_FiberDirection; ///< Needed to generate anisotropc signal to determin direction of anisotropy GradientListType m_GradientList; ///< Diffusion gradient direction container double m_T2; ///< Tissue specific relaxation time double m_Weight; }; } #endif diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index d1b25735d7..44b4d5e239 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,1514 +1,1574 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_SelectedBundle( NULL ) { } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); + m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); + m_Controls->m_VarianceBox->setVisible(false); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberSamplingChanged(int))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGibbsRinging(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddGibbsRinging(int value) { if (value>0) m_Controls->m_KspaceParamFrame->setVisible(true); else m_Controls->m_KspaceParamFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for( int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for( int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/10; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundle = node; m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundle.IsNull()) OnAddBundle(); if (m_SelectedBundle.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundle); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); GetDataStorage()->Add(node, m_SelectedBundle); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); UpdateGui(); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (fib.size()<3) return; } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { itk::ImageRegion<3> imageRegion; imageRegion.SetSize(0, m_Controls->m_SizeX->value()); imageRegion.SetSize(1, m_Controls->m_SizeY->value()); imageRegion.SetSize(2, m_Controls->m_SizeZ->value()); mitk::Vector3D spacing; spacing[0] = m_Controls->m_SpacingX->value(); spacing[1] = m_Controls->m_SpacingY->value(); spacing[2] = m_Controls->m_SpacingZ->value(); mitk::Point3D origin; origin[0] = spacing[0]/2; origin[1] = spacing[1]/2; origin[2] = spacing[2]/2; itk::Matrix directionMatrix; directionMatrix.SetIdentity(); if (m_SelectedBundle.IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Geometry3D* geom = image->GetGeometry(); geom->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); + unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); + unsigned int level = window/2; + node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( mitk::LevelWindow(level, window) ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); return; } DiffusionSignalModel::GradientListType gradientList; double bVal = 1000; if (m_SelectedDWI.IsNull()) { gradientList = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());; bVal = m_Controls->m_BvalueBox->value(); } else { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); spacing = dwi->GetVectorImage()->GetSpacing(); origin = dwi->GetVectorImage()->GetOrigin(); directionMatrix = dwi->GetVectorImage()->GetDirection(); bVal = dwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); for (int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; gradientList.push_back(g); } } for (int i=0; im_Compartment4Box->currentIndex()>0) { comp4Weight = m_Controls->m_Comp4FractionBox->value(); comp3Weight -= comp4Weight; } mitk::StickModel stickModel1; mitk::StickModel stickModel2; mitk::TensorModel zeppelinModel1; mitk::TensorModel zeppelinModel2; mitk::TensorModel tensorModel1; mitk::TensorModel tensorModel2; mitk::BallModel ballModel1; mitk::BallModel ballModel2; mitk::AstroStickModel astrosticksModel1; mitk::AstroStickModel astrosticksModel2; mitk::DotModel dotModel1; mitk::DotModel dotModel2; // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: MITK_INFO << "Using stick model"; stickModel1.SetGradientList(gradientList); stickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); stickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); fiberModelList.push_back(&stickModel1); signalModelString += "Stick"; -// resultNode->AddProperty("Fiberfox.Stick.Diffusivity", DoubleProperty::New(m_Controls->m_StickWidget1->GetD())); -// resultNode->AddProperty("Fiberfox.Stick.T2", DoubleProperty::New(stickModel1.GetT2())); + resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); + resultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(stickModel1.GetT2()) ); break; case 1: MITK_INFO << "Using zeppelin model"; zeppelinModel1.SetGradientList(gradientList); zeppelinModel1.SetBvalue(bVal); zeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); zeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); fiberModelList.push_back(&zeppelinModel1); signalModelString += "Zeppelin"; + resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); + resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); + resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); + resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; case 2: MITK_INFO << "Using tensor model"; tensorModel1.SetGradientList(gradientList); tensorModel1.SetBvalue(bVal); tensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); tensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); tensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); tensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); fiberModelList.push_back(&tensorModel1); signalModelString += "Tensor"; + resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); + resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); + resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); + resultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); + resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: stickModel2.SetGradientList(gradientList); stickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); stickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); fiberModelList.push_back(&stickModel2); signalModelString += "Stick"; + resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); + resultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(stickModel2.GetT2()) ); break; case 2: zeppelinModel2.SetGradientList(gradientList); zeppelinModel2.SetBvalue(bVal); zeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); zeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); fiberModelList.push_back(&zeppelinModel2); signalModelString += "Zeppelin"; + resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); + resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); + resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); + resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; case 3: tensorModel2.SetGradientList(gradientList); tensorModel2.SetBvalue(bVal); tensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); tensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); tensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); tensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); fiberModelList.push_back(&tensorModel2); signalModelString += "Tensor"; + resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); + resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); + resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); + resultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); + resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: ballModel1.SetGradientList(gradientList); ballModel1.SetBvalue(bVal); ballModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); ballModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); ballModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&ballModel1); signalModelString += "Ball"; + resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); + resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(ballModel1.GetT2()) ); break; case 1: astrosticksModel1.SetGradientList(gradientList); astrosticksModel1.SetBvalue(bVal); astrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); astrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); astrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); astrosticksModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&astrosticksModel1); signalModelString += "Astrosticks"; + resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); + resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(astrosticksModel1.GetT2()) ); + resultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: dotModel1.SetGradientList(gradientList); dotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); dotModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&dotModel1); signalModelString += "Dot"; + resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); + resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(dotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: ballModel2.SetGradientList(gradientList); ballModel2.SetBvalue(bVal); ballModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); ballModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); ballModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&ballModel2); signalModelString += "Ball"; + resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); + resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(ballModel2.GetT2()) ); break; case 2: astrosticksModel2.SetGradientList(gradientList); astrosticksModel2.SetBvalue(bVal); astrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); astrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); astrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); astrosticksModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&astrosticksModel2); signalModelString += "Astrosticks"; + resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); + resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); + resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(astrosticksModel2.GetT2()) ); + resultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: dotModel2.SetGradientList(gradientList); dotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); dotModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&dotModel2); signalModelString += "Dot"; + resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); + resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(dotModel2.GetT2()) ); break; } itk::TractsToDWIImageFilter::KspaceArtifactList artifactList; // noise model double noiseVariance = m_Controls->m_NoiseLevel->value(); mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); // artifact models QString artifactModelString(""); mitk::GibbsRingingArtifact gibbsModel; if (m_Controls->m_AddGibbsRinging->isChecked()) { artifactModelString += "_Gibbs-ringing"; resultNode->AddProperty("Fiberfox.k-Space-Undersampling", IntProperty::New(m_Controls->m_KspaceUndersamplingBox->currentText().toInt())); gibbsModel.SetKspaceCropping((double)m_Controls->m_KspaceUndersamplingBox->currentText().toInt()); artifactList.push_back(&gibbsModel); } mitk::T2SmearingArtifact contrastModel; contrastModel.SetT2star(this->m_Controls->m_T2starBox->value()); contrastModel.SetTE(this->m_Controls->m_TEbox->value()); contrastModel.SetTline(m_Controls->m_LineReadoutTimeBox->value()); artifactList.push_back(&contrastModel); mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(m_SelectedBundles.at(i)->GetData()); if (fiberBundle->GetNumFibers()<=0) continue; itk::TractsToDWIImageFilter::Pointer filter = itk::TractsToDWIImageFilter::New(); filter->SetImageRegion(imageRegion); filter->SetSpacing(spacing); filter->SetOrigin(origin); filter->SetDirectionMatrix(directionMatrix); filter->SetFiberBundle(fiberBundle); filter->SetFiberModels(fiberModelList); filter->SetNonFiberModels(nonFiberModelList); filter->SetNoiseModel(&noiseModel); filter->SetKspaceArtifacts(artifactList); filter->SetNumberOfRepetitions(m_Controls->m_RepetitionsBox->value()); filter->SetEnforcePureFiberVoxels(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked()); filter->SetInterpolationShrink(m_Controls->m_InterpolationShrink->value()); filter->SetFiberRadius(m_Controls->m_FiberRadius->value()); filter->SetSignalScale(m_Controls->m_SignalScaleBox->value()); if (m_TissueMask.IsNotNull()) { ItkUcharImgType::Pointer mask = ItkUcharImgType::New(); mitk::CastToItkImage(m_TissueMask, mask); filter->SetTissueMask(mask); } filter->Update(); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedBundles.at(i)->GetName() +"_D"+QString::number(imageRegion.GetSize(0)).toStdString() +"-"+QString::number(imageRegion.GetSize(1)).toStdString() +"-"+QString::number(imageRegion.GetSize(2)).toStdString() +"_S"+QString::number(spacing[0]).toStdString() +"-"+QString::number(spacing[1]).toStdString() +"-"+QString::number(spacing[2]).toStdString() +"_b"+QString::number(bVal).toStdString() +"_NOISE"+QString::number(noiseVariance).toStdString() +"_"+signalModelString.toStdString() +artifactModelString.toStdString()); GetDataStorage()->Add(resultNode, m_SelectedBundles.at(i)); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); resultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_Controls->m_RepetitionsBox->value())); resultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(bVal)); resultNode->AddProperty("Fiberfox.Model", StringProperty::New(signalModelString.toStdString())); + resultNode->AddProperty("binary", BoolProperty::New(false)); + resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(filter->GetLevelWindow()) ); if (m_Controls->m_KspaceImageBox->isChecked()) { itk::Image::Pointer kspace = filter->GetKspaceImage(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(kspace.GetPointer()); image->SetVolume(kspace->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(m_SelectedBundles.at(i)->GetName()+"_k-space"); GetDataStorage()->Add(node, m_SelectedBundles.at(i)); } mitk::BaseData::Pointer basedata = resultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for( int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); } } } } } else { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); for (it; it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || m_SelectedBundle.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_TissueMask.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedBundle.IsNotNull()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundle->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_TissueMask = NULL; m_SelectedBundles.clear(); m_SelectedBundle = NULL; m_SelectedImage = NULL; m_SelectedDWI = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_TissueMask = dynamic_cast(node->GetData()); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked() && node!=m_SelectedBundle) { m_SelectedBundle = node; m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else { m_SelectedBundle = node; m_SelectedBundles.push_back(node); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) { m_SelectedBundle = pNode; m_SelectedBundles.push_back(pNode); } } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { if (node == m_SelectedImage) m_SelectedImage = NULL; if (node == m_SelectedBundle) m_SelectedBundle = NULL; mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", nonConstNode); } else { // just to be sure that the interactor is not added twice mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } MITK_DEBUG << "adding interactor to globalinteraction"; mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } 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 813300bbbf..574fcd950b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2033 +1,2033 @@ QmitkFiberfoxViewControls 0 0 493 1438 Form 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 Copy Bundles false Transform Selection QFrame::NoFrame QFrame::Raised 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 Join Bundles If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Fiber sampling points (per cm) 1 100 1 10 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 QFrame::NoFrame QFrame::Raised 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 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 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 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 - + Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model 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 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 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 Image Settings QFrame::NoFrame QFrame::Raised 0 6 Fiber Radius: Output k-Space Image false Treat voxel content as fiber-only if at least one fiber is present. Enforce Pure Fiber Voxels false Repetitions: Number of signal averages. Increase to reduce noise. 1 100 1 1 T2* Relaxation: false Scaling factor for signal. 0 10000 1 200 Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1 10000 10 Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 T2* relaxation time (in milliseconds). 1 10000 1 50 Interpolation Shrink: TE in milliseconds 1 10000 1 100 Signal Scale: false Echo Time TE: false Line Readout Time: false T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 color: rgb(255, 0, 0); Using mask image geometry! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 3 0.100000000000000 50.000000000000000 0.100000000000000 - 2.500000000000000 + 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 - 2.500000000000000 + 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 - 2.500000000000000 + 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 - 32 + 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 100 1 - 32 + 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 100 1 - 5 + 3 QFrame::NoFrame QFrame::Raised 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options Qt::Vertical 20 40 Noise and Artifacts true QFrame::NoFrame QFrame::Raised 6 0 k-Space Undersampling: false Image is upsampled using this factor, afterwards fourier transformed, cropped to the original size and then inverse fourier transformed. 0 2 4 8 16 32 64 128 256 true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 0 0 0 QFrame::NoFrame QFrame::Raised 0 Variance: Variance of Rician noise model. 4 0.000000000000000 100000.000000000000000 0.001000000000000 25.000000000000000 Add Gibbs Ringing false Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model 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 tabWidget m_CircleButton m_FlipButton m_RealTimeFibers m_DistributionBox m_AdvancedOptionsBox 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_EnforcePureFiberVoxelsBox m_KspaceImageBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_NoiseLevel m_AddGibbsRinging m_KspaceUndersamplingBox