diff --git a/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.cpp index 28f51c8bd2..4aa8b875c8 100644 --- a/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.cpp +++ b/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.cpp @@ -1,699 +1,718 @@ /*=================================================================== 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 __itkStreamlineTrackingFilter_txx #define __itkStreamlineTrackingFilter_txx #include #include #include #include "itkStreamlineTrackingFilter.h" #include #include #include #define _USE_MATH_DEFINES #include namespace itk { //#define QBALL_RECON_PI M_PI template< class TTensorPixelType, class TPDPixelType> StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::StreamlineTrackingFilter(): m_FaThreshold(0.2), m_StepSize(1), m_MaxLength(10000), m_SeedsPerVoxel(1), - m_AngularThreshold(0.7), m_F(1.0), m_G(0.0), m_Interpolate(true), m_MinTractLength(0.0) { // At least 1 inputs is necessary for a vector image. // For images added one at a time we need at least six this->SetNumberOfRequiredInputs( 1 ); } template< class TTensorPixelType, class TPDPixelType> double StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::BeforeThreadedGenerateData() { m_FiberPolyData = FiberPolyDataType::New(); m_Points = vtkPoints::New(); m_Cells = vtkCellArray::New(); m_InputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); m_ImageSize.resize(3); m_ImageSize[0] = m_InputImage->GetLargestPossibleRegion().GetSize()[0]; m_ImageSize[1] = m_InputImage->GetLargestPossibleRegion().GetSize()[1]; m_ImageSize[2] = m_InputImage->GetLargestPossibleRegion().GetSize()[2]; if (m_ImageSize[0]<3 || m_ImageSize[1]<3 || m_ImageSize[2]<3) m_Interpolate = false; m_ImageSpacing.resize(3); m_ImageSpacing[0] = m_InputImage->GetSpacing()[0]; m_ImageSpacing[1] = m_InputImage->GetSpacing()[1]; m_ImageSpacing[2] = m_InputImage->GetSpacing()[2]; float minSpacing; if(m_ImageSpacing[0]::New(); for (int i=0; iGetNumberOfThreads(); i++) { FiberPolyDataType poly = FiberPolyDataType::New(); m_PolyDataContainer->InsertElement(i, poly); } if (m_SeedImage.IsNull()) { // initialize mask image m_SeedImage = ItkUcharImgType::New(); m_SeedImage->SetSpacing( m_InputImage->GetSpacing() ); m_SeedImage->SetOrigin( m_InputImage->GetOrigin() ); m_SeedImage->SetDirection( m_InputImage->GetDirection() ); m_SeedImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); m_SeedImage->Allocate(); m_SeedImage->FillBuffer(1); } if (m_MaskImage.IsNull()) { // initialize mask image m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( m_InputImage->GetSpacing() ); m_MaskImage->SetOrigin( m_InputImage->GetOrigin() ); m_MaskImage->SetDirection( m_InputImage->GetDirection() ); m_MaskImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } m_FaImage = ItkFloatImgType::New(); m_FaImage->SetSpacing( m_InputImage->GetSpacing() ); m_FaImage->SetOrigin( m_InputImage->GetOrigin() ); m_FaImage->SetDirection( m_InputImage->GetDirection() ); m_FaImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); m_FaImage->Allocate(); m_FaImage->FillBuffer(0.0); m_PdImage = ItkPDImgType::New(); m_PdImage->SetSpacing( m_InputImage->GetSpacing() ); m_PdImage->SetOrigin( m_InputImage->GetOrigin() ); m_PdImage->SetDirection( m_InputImage->GetDirection() ); m_PdImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); m_PdImage->Allocate(); m_EmaxImage = ItkFloatImgType::New(); m_EmaxImage->SetSpacing( m_InputImage->GetSpacing() ); m_EmaxImage->SetOrigin( m_InputImage->GetOrigin() ); m_EmaxImage->SetDirection( m_InputImage->GetDirection() ); m_EmaxImage->SetRegions( m_InputImage->GetLargestPossibleRegion() ); m_EmaxImage->Allocate(); m_EmaxImage->FillBuffer(1.0); typedef itk::DiffusionTensor3D TensorType; typename TensorType::EigenValuesArrayType eigenvalues; typename TensorType::EigenVectorsMatrixType eigenvectors; for (int x=0; xGetPixel(index); vnl_vector_fixed dir; tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); dir.normalize(); m_PdImage->SetPixel(index, dir); m_FaImage->SetPixel(index, tensor.GetFractionalAnisotropy()); m_EmaxImage->SetPixel(index, 2/eigenvalues[2]); } - std::cout << "StreamlineTrackingFilter: Angular threshold: " << m_AngularThreshold << std::endl; - std::cout << "StreamlineTrackingFilter: FA threshold: " << m_FaThreshold << std::endl; - std::cout << "StreamlineTrackingFilter: stepsize: " << m_StepSize << " mm" << std::endl; - std::cout << "StreamlineTrackingFilter: f: " << m_F << std::endl; - std::cout << "StreamlineTrackingFilter: g: " << m_G << std::endl; if (m_Interpolate) std::cout << "StreamlineTrackingFilter: using trilinear interpolation" << std::endl; else + { + if (m_MinCurvatureRadius<0.0) + m_MinCurvatureRadius = 0.1*minSpacing; + std::cout << "StreamlineTrackingFilter: using nearest neighbor interpolation" << std::endl; + } + + if (m_MinCurvatureRadius<0.0) + m_MinCurvatureRadius = 0.5*minSpacing; + + std::cout << "StreamlineTrackingFilter: Min. curvature radius: " << m_MinCurvatureRadius << std::endl; + std::cout << "StreamlineTrackingFilter: FA threshold: " << m_FaThreshold << std::endl; + std::cout << "StreamlineTrackingFilter: stepsize: " << m_StepSize << " mm" << std::endl; + std::cout << "StreamlineTrackingFilter: f: " << m_F << std::endl; + std::cout << "StreamlineTrackingFilter: g: " << m_G << std::endl; std::cout << "StreamlineTrackingFilter: starting streamline tracking" << std::endl; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::CalculateNewPosition(itk::ContinuousIndex& pos, vnl_vector_fixed& dir, typename InputImageType::IndexType& index) { if (true) { dir *= m_StepSize; pos[0] += dir[0]/m_ImageSpacing[0]; pos[1] += dir[1]/m_ImageSpacing[1]; pos[2] += dir[2]/m_ImageSpacing[2]; index[0] = RoundToNearest(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); } else { dir[0] /= m_ImageSpacing[0]; dir[1] /= m_ImageSpacing[1]; dir[2] /= m_ImageSpacing[2]; int smallest = 0; float x = 100000; if (dir[0]>0) { if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps) x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0]; else x = fabs(pos[0]-std::ceil(pos[0])-0.5)/dir[0]; } else if (dir[0]<0) { if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps) x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0]; else x = -fabs(pos[0]-std::floor(pos[0])+0.5)/dir[0]; } float s = x; float y = 100000; if (dir[1]>0) { if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps) y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1]; else y = fabs(pos[1]-std::ceil(pos[1])-0.5)/dir[1]; } else if (dir[1]<0) { if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps) y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1]; else y = -fabs(pos[1]-std::floor(pos[1])+0.5)/dir[1]; } if (s>y) { s=y; smallest = 1; } float z = 100000; if (dir[2]>0) { if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps) z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2]; else z = fabs(pos[2]-std::ceil(pos[2])-0.5)/dir[2]; } else if (dir[2]<0) { if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps) z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2]; else z = -fabs(pos[2]-std::floor(pos[2])+0.5)/dir[2]; } if (s>z) { s=z; smallest = 2; } // MITK_INFO << "---------------------------------------------"; // MITK_INFO << "s: " << s; // MITK_INFO << "dir: " << dir; // MITK_INFO << "old: " << pos[0] << ", " << pos[1] << ", " << pos[2]; pos[0] += dir[0]*s; pos[1] += dir[1]*s; pos[2] += dir[2]*s; switch (smallest) { case 0: if (dir[0]<0) index[0] = std::floor(pos[0]); else index[0] = std::ceil(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); break; case 1: if (dir[1]<0) index[1] = std::floor(pos[1]); else index[1] = std::ceil(pos[1]); index[0] = RoundToNearest(pos[0]); index[2] = RoundToNearest(pos[2]); break; case 2: if (dir[2]<0) index[2] = std::floor(pos[2]); else index[2] = std::ceil(pos[2]); index[1] = RoundToNearest(pos[1]); index[0] = RoundToNearest(pos[0]); } // float x = 100000; // if (dir[0]>0) // x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0]; // else if (dir[0]<0) // x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0]; // float s = x; // float y = 100000; // if (dir[1]>0) // y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1]; // else if (dir[1]<0) // y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1]; // if (s>y) // s=y; // float z = 100000; // if (dir[2]>0) // z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2]; // else if (dir[2]<0) // z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2]; // if (s>z) // s=z; // s *= 1.001; // pos[0] += dir[0]*s; // pos[1] += dir[1]*s; // pos[2] += dir[2]*s; // index[0] = RoundToNearest(pos[0]); // index[1] = RoundToNearest(pos[1]); // index[2] = RoundToNearest(pos[2]); // MITK_INFO << "new: " << pos[0] << ", " << pos[1] << ", " << pos[2]; } } template< class TTensorPixelType, class TPDPixelType> bool StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::IsValidPosition(itk::ContinuousIndex& pos, typename InputImageType::IndexType &index, vnl_vector_fixed< float, 8 >& interpWeights) { if (m_MaskImage->GetPixel(index)==0 || !m_InputImage->GetLargestPossibleRegion().IsInside(index)) return false; if (m_Interpolate) { float frac_x = pos[0] - index[0]; float frac_y = pos[1] - index[1]; float frac_z = pos[2] - index[2]; if (frac_x<0) { index[0] -= 1; frac_x += 1; } if (frac_y<0) { index[1] -= 1; frac_y += 1; } if (frac_z<0) { index[2] -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (index[0] < 0 || index[0] >= m_ImageSize[0]-1) return false; if (index[1] < 0 || index[1] >= m_ImageSize[1]-1) return false; if (index[2] < 0 || index[2] >= m_ImageSize[2]-1) return false; interpWeights[0] = ( frac_x)*( frac_y)*( frac_z); interpWeights[1] = (1-frac_x)*( frac_y)*( frac_z); interpWeights[2] = ( frac_x)*(1-frac_y)*( frac_z); interpWeights[3] = ( frac_x)*( frac_y)*(1-frac_z); interpWeights[4] = (1-frac_x)*(1-frac_y)*( frac_z); interpWeights[5] = ( frac_x)*(1-frac_y)*(1-frac_z); interpWeights[6] = (1-frac_x)*( frac_y)*(1-frac_z); interpWeights[7] = (1-frac_x)*(1-frac_y)*(1-frac_z); typename InputImageType::IndexType tmpIdx; float FA = m_FaImage->GetPixel(index) * interpWeights[0]; tmpIdx = index; tmpIdx[0]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[1]; tmpIdx = index; tmpIdx[1]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[2]; tmpIdx = index; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[3]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[4]; tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[5]; tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[6]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[7]; if (FAGetPixel(index) float StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids) { float tractLength = 0; typedef itk::DiffusionTensor3D TensorType; typename TensorType::EigenValuesArrayType eigenvalues; typename TensorType::EigenVectorsMatrixType eigenvectors; vnl_vector_fixed< float, 8 > interpWeights; typename InputImageType::IndexType index, indexOld; indexOld[0] = -1; indexOld[1] = -1; indexOld[2] = -1; itk::Point worldPos; float distance = 0; + float distanceInVoxel = 0; // starting index and direction index[0] = RoundToNearest(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); vnl_vector_fixed dir = m_PdImage->GetPixel(index); dir *= dirSign; // reverse direction vnl_vector_fixed dirOld = dir; if (dir.magnitude()TransformContinuousIndexToPhysicalPoint( pos, worldPos ); ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer())); return tractLength; } else if (distance>=m_PointPistance) { m_InputImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos ); ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer())); distance = 0; } if (!m_Interpolate) // use nearest neighbour interpolation { if (indexOld!=index) // did we enter a new voxel? if yes, calculate new direction { dir = m_PdImage->GetPixel(index); // get principal direction typename InputImageType::PixelType tensor = m_InputImage->GetPixel(index); float scale = m_EmaxImage->GetPixel(index); dir[0] = m_F*dir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2])); dir[1] = m_F*dir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2])); dir[2] = m_F*dir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2])); dir.normalize(); float angle = dot_product(dirOld, dir); if (angle<0) + { dir *= -1; - angle = dot_product(dirOld, dir); - if (angleGetPixel(index) * interpWeights[0]; typename InputImageType::IndexType tmpIdx = index; tmpIdx[0]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[1]; tmpIdx = index; tmpIdx[1]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[2]; tmpIdx = index; tmpIdx[2]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[3]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[4]; tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[5]; tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[6]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[7]; tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); dir.normalize(); float scale = 2/eigenvalues[2]; dir[0] = m_F*dir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2])); dir[1] = m_F*dir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2])); dir[2] = m_F*dir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2])); dir.normalize(); float angle = dot_product(dirOld, dir); if (angle<0) + { dir *= -1; - angle = dot_product(dirOld, dir); - if (angle void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId) { FiberPolyDataType poly = m_PolyDataContainer->GetElement(threadId); vtkSmartPointer points = vtkPoints::New(); vtkSmartPointer Cells = vtkCellArray::New(); typedef itk::DiffusionTensor3D TensorType; typedef ImageRegionConstIterator< InputImageType > InputIteratorType; typedef ImageRegionConstIterator< ItkUcharImgType > MaskIteratorType; typedef ImageRegionConstIterator< ItkFloatImgType > FloatIteratorType; typedef typename InputImageType::PixelType InputTensorType; InputIteratorType it(m_InputImage, outputRegionForThread ); MaskIteratorType mit(m_SeedImage, outputRegionForThread ); FloatIteratorType fit(m_FaImage, outputRegionForThread ); MaskIteratorType mit2(m_MaskImage, outputRegionForThread ); it.GoToBegin(); mit.GoToBegin(); mit2.GoToBegin(); fit.GoToBegin(); itk::Point worldPos; while( !it.IsAtEnd() ) { if (mit.Value()==0 || fit.Value() line = vtkSmartPointer::New(); std::vector< vtkIdType > pointIDs; typename InputImageType::IndexType index = it.GetIndex(); itk::ContinuousIndex start; unsigned int counter = 0; if (m_SeedsPerVoxel>1) { start[0] = index[0]+(double)(rand()%99-49)/100; start[1] = index[1]+(double)(rand()%99-49)/100; start[2] = index[2]+(double)(rand()%99-49)/100; } else { start[0] = index[0]; start[1] = index[1]; start[2] = index[2]; } // forward tracking float tractLength = FollowStreamline(start, 1, points, pointIDs); // add ids to line counter += pointIDs.size(); while (!pointIDs.empty()) { line->GetPointIds()->InsertNextId(pointIDs.back()); pointIDs.pop_back(); } // insert start point m_InputImage->TransformContinuousIndexToPhysicalPoint( start, worldPos ); line->GetPointIds()->InsertNextId(points->InsertNextPoint(worldPos.GetDataPointer())); // backward tracking tractLength += FollowStreamline(start, -1, points, pointIDs); counter += pointIDs.size(); if (tractLengthGetPointIds()->InsertNextId(pointIDs.at(i)); Cells->InsertNextCell(line); } ++mit; ++mit2; ++it; ++fit; } poly->SetPoints(points); poly->SetLines(Cells); std::cout << "Thread " << threadId << " finished tracking" << std::endl; } template< class TTensorPixelType, class TPDPixelType> vtkSmartPointer< vtkPolyData > StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::AddPolyData(FiberPolyDataType poly1, FiberPolyDataType poly2) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = poly1->GetLines(); vtkSmartPointer vNewPoints = poly1->GetPoints(); vtkSmartPointer vLines = poly2->GetLines(); vLines->InitTraversal(); for( int i=0; iGetNumberOfCells(); i++ ) { vtkIdType numPoints(0); vtkIdType* points(NULL); vLines->GetNextCell ( numPoints, points ); vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(poly2->GetPoint(points[j])); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); return vNewPolyData; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::AfterThreadedGenerateData() { MITK_INFO << "Generating polydata "; m_FiberPolyData = m_PolyDataContainer->GetElement(0); for (int i=1; iGetNumberOfThreads(); i++) { m_FiberPolyData = AddPolyData(m_FiberPolyData, m_PolyDataContainer->GetElement(i)); } MITK_INFO << "done"; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::PrintSelf(std::ostream& os, Indent indent) const { } } #endif // __itkDiffusionQballPrincipleDirectionsImageFilter_txx diff --git a/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.h b/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.h index acbf55ee12..ec6b509428 100644 --- a/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.h +++ b/Modules/DiffusionImaging/Tractography/itkStreamlineTrackingFilter.h @@ -1,136 +1,137 @@ /*=================================================================== 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 __itkStreamlineTrackingFilter_h_ #define __itkStreamlineTrackingFilter_h_ #include "MitkDiffusionImagingExports.h" #include #include #include #include #include #include #include #include #include namespace itk{ /** \class StreamlineTrackingFilter */ template< class TTensorPixelType, class TPDPixelType=double> class StreamlineTrackingFilter : public ImageToImageFilter< Image< DiffusionTensor3D, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > { public: typedef StreamlineTrackingFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< Image< DiffusionTensor3D, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > Superclass; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(StreamlineTrackingFilter, ImageToImageFilter) typedef TTensorPixelType TensorComponentType; typedef TPDPixelType DirectionPixelType; typedef typename Superclass::InputImageType InputImageType; typedef typename Superclass::OutputImageType OutputImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; typedef itk::Image ItkUcharImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image< vnl_vector_fixed, 3> ItkPDImgType; typedef vtkSmartPointer< vtkPolyData > FiberPolyDataType; itkGetMacro( FiberPolyData, FiberPolyDataType ) itkSetMacro( SeedImage, ItkUcharImgType::Pointer) itkSetMacro( MaskImage, ItkUcharImgType::Pointer) itkSetMacro( SeedsPerVoxel, int) itkSetMacro( FaThreshold, float) - itkSetMacro( AngularThreshold, float) itkSetMacro( StepSize, float) itkSetMacro( F, float ) itkSetMacro( G, float ) itkSetMacro( Interpolate, bool ) itkSetMacro( MinTractLength, float ) itkGetMacro( MinTractLength, float ) + itkSetMacro( MinCurvatureRadius, float ) + itkGetMacro( MinCurvatureRadius, float ) protected: StreamlineTrackingFilter(); ~StreamlineTrackingFilter() {} void PrintSelf(std::ostream& os, Indent indent) const; void CalculateNewPosition(itk::ContinuousIndex& pos, vnl_vector_fixed& dir, typename InputImageType::IndexType& index); float FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids); bool IsValidPosition(itk::ContinuousIndex& pos, typename InputImageType::IndexType& index, vnl_vector_fixed< float, 8 >& interpWeights); double RoundToNearest(double num); void BeforeThreadedGenerateData(); void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, int threadId); void AfterThreadedGenerateData(); FiberPolyDataType AddPolyData(FiberPolyDataType poly1, FiberPolyDataType poly2); FiberPolyDataType m_FiberPolyData; vtkSmartPointer m_Points; vtkSmartPointer m_Cells; ItkFloatImgType::Pointer m_EmaxImage; ItkFloatImgType::Pointer m_FaImage; ItkPDImgType::Pointer m_PdImage; typename InputImageType::Pointer m_InputImage; float m_FaThreshold; - float m_AngularThreshold; + float m_MinCurvatureRadius; float m_StepSize; int m_MaxLength; float m_MinTractLength; int m_SeedsPerVoxel; float m_F; float m_G; std::vector< int > m_ImageSize; std::vector< float > m_ImageSpacing; ItkUcharImgType::Pointer m_SeedImage; ItkUcharImgType::Pointer m_MaskImage; bool m_Interpolate; float m_PointPistance; itk::VectorContainer< int, FiberPolyDataType >::Pointer m_PolyDataContainer; private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkStreamlineTrackingFilter.cpp" #endif #endif //__itkStreamlineTrackingFilter_h_ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp index 4b283b73c2..2e56751c9c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp @@ -1,239 +1,242 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkStreamlineTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include #include // VTK #include #include #include #include #include #include const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStreamlineTrackingView::QmitkStreamlineTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_TensorImage( NULL ) , m_SeedRoi( NULL ) { } // Destructor QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView() { } void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStreamlineTrackingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_SeedsPerVoxelSlider, SIGNAL(valueChanged(int)), this, SLOT(OnSeedsPerVoxelChanged(int)) ); connect( m_Controls->m_MinTractLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMinTractLengthChanged(int)) ); connect( m_Controls->m_FaThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnFaThresholdChanged(int)) ); connect( m_Controls->m_AngularThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAngularThresholdChanged(int)) ); connect( m_Controls->m_StepsizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnStepsizeChanged(int)) ); connect( m_Controls->m_fSlider, SIGNAL(valueChanged(int)), this, SLOT(OnfChanged(int)) ); connect( m_Controls->m_gSlider, SIGNAL(valueChanged(int)), this, SLOT(OngChanged(int)) ); } } void QmitkStreamlineTrackingView::OnfChanged(int value) { m_Controls->m_fLabel->setText(QString("f: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OngChanged(int value) { m_Controls->m_gLabel->setText(QString("g: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OnAngularThresholdChanged(int value) { - m_Controls->m_AngularThresholdLabel->setText(QString("Angular Threshold: ")+QString::number(value)+QString("°")); + if (value<0) + m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: auto")); + else + m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: ")+QString::number((float)value/10)+QString("mm")); } void QmitkStreamlineTrackingView::OnSeedsPerVoxelChanged(int value) { m_Controls->m_SeedsPerVoxelLabel->setText(QString("Seeds per Voxel: ")+QString::number(value)); } void QmitkStreamlineTrackingView::OnMinTractLengthChanged(int value) { m_Controls->m_MinTractLengthLabel->setText(QString("Min. Tract Length: ")+QString::number(value)+QString("mm")); } void QmitkStreamlineTrackingView::OnFaThresholdChanged(int value) { m_Controls->m_FaThresholdLabel->setText(QString("FA Threshold: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OnStepsizeChanged(int value) { if (value==0) m_Controls->m_StepsizeLabel->setText(QString("Stepsize: auto")); else m_Controls->m_StepsizeLabel->setText(QString("Stepsize: ")+QString::number((float)value/10)+QString("mm")); } void QmitkStreamlineTrackingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkStreamlineTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkStreamlineTrackingView::OnSelectionChanged( std::vector nodes ) { m_TensorImageNode = NULL; m_TensorImage = NULL; m_SeedRoi = NULL; m_MaskImage = NULL; m_Controls->m_TensorImageLabel->setText("-"); m_Controls->m_RoiImageLabel->setText("-"); m_Controls->m_MaskImageLabel->setText("-"); if(nodes.empty()) return; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) ) { m_TensorImageNode = node; m_TensorImage = dynamic_cast(node->GetData()); m_Controls->m_TensorImageLabel->setText(node->GetName().c_str()); } else { bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary && m_SeedRoi.IsNull()) { m_SeedRoi = dynamic_cast(node->GetData()); m_Controls->m_RoiImageLabel->setText(node->GetName().c_str()); } else if (isBinary) { m_MaskImage = dynamic_cast(node->GetData()); m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); } } } } if(m_TensorImage.IsNotNull()) m_Controls->commandLinkButton->setEnabled(true); else m_Controls->commandLinkButton->setEnabled(false); } void QmitkStreamlineTrackingView::DoFiberTracking() { if (m_TensorImage.IsNull()) return; typedef itk::Image< itk::DiffusionTensor3D, 3> TensorImageType; typedef mitk::ImageToItk CastType; typedef mitk::ImageToItk CastType2; CastType::Pointer caster = CastType::New(); caster->SetInput(m_TensorImage); caster->Update(); TensorImageType::Pointer image = caster->GetOutput(); typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(image); filter->SetSeedsPerVoxel(m_Controls->m_SeedsPerVoxelSlider->value()); filter->SetFaThreshold((float)m_Controls->m_FaThresholdSlider->value()/100); - filter->SetAngularThreshold(cos((float)m_Controls->m_AngularThresholdSlider->value()*M_PI/180)); + filter->SetMinCurvatureRadius((float)m_Controls->m_AngularThresholdSlider->value()/10); filter->SetStepSize((float)m_Controls->m_StepsizeSlider->value()/10); filter->SetF((float)m_Controls->m_fSlider->value()/100); filter->SetG((float)m_Controls->m_gSlider->value()/100); filter->SetInterpolate(m_Controls->m_InterpolationBox->isChecked()); filter->SetMinTractLength(m_Controls->m_MinTractLengthSlider->value()); //filter->SetNumberOfThreads(1); if (m_SeedRoi.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(m_SeedRoi, mask); filter->SetSeedImage(mask); } if (m_MaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(m_MaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer fiberBundle = filter->GetFiberPolyData(); if ( fiberBundle->GetNumberOfLines()==0 ) return; mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name(m_TensorImageNode->GetName().c_str()); name += "_Streamline"; node->SetName(name.toStdString()); node->SetVisibility(true); GetDataStorage()->Add(node); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui index aa5e2fb2bf..740ff63c5f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui @@ -1,385 +1,388 @@ QmitkStreamlineTrackingViewControls 0 0 480 553 0 0 QmitkTemplate 3 3 0 Qt::Vertical QSizePolicy::Expanding 20 220 Parameters Number of tracts started in each voxel of the seed ROI. 1 100 Qt::Horizontal - Fractional Anisotropy Threshold + Minimally allowed curcature radius (in mm, interpolated auto = 0.5 minimal spacing, noninterpolated auto = 0.1 minimal spacing) - 0 + -1 - 90 + 50 - 45 + -1 Qt::Horizontal Minimum tract length in mm. 0 500 40 Qt::Horizontal - Number of tracts started in each voxel of the seed ROI. + Seeds per Voxel: 1 Qt::Horizontal QSizePolicy::Fixed 200 0 Fractional Anisotropy Threshold 0 100 20 Qt::Horizontal Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0). 0 100 100 Qt::Horizontal - Minimum tract length in mm. + FA Threshold: 0.2 - Minimum tract length in mm. + Min. Tract Length: 40mm Stepsize in mm (auto = 0.1*minimal spacing) 0 100 0 Qt::Horizontal - Minimum tract length in mm. + g: 0 Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking) 0 100 0 Qt::Horizontal - Minimum tract length in mm. + - Angular Threshold: 45° + Min. Curvature Radius: auto - Minimum tract length in mm. + Step Size: auto - Minimum tract length in mm. + f: 1 Default is nearest neighbor interpolation. Enable trilinear interpolation + + false + Number of tracts started in each voxel of the seed ROI. Mori et al. Annals Neurology 1999 false Start Tracking Data - - Seed ROI Image: Tensor Image: Stop tracking if leaving mask Mask Image: - Number of tracts started in each voxel of the seed ROI. Lazar et al. Human Brain Mapping 2003 Number of tracts started in each voxel of the seed ROI. Weinstein et al. Proceedings of IEEE Visualization 1999 commandLinkButton