diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp index b8ac12b6c0..8279690c85 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp @@ -1,271 +1,276 @@ /*=================================================================== 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 "mitkTrackingHandlerPeaks.h" namespace mitk { TrackingHandlerPeaks::TrackingHandlerPeaks() : m_PeakThreshold(0.1) , m_ApplyDirectionMatrix(false) { } TrackingHandlerPeaks::~TrackingHandlerPeaks() { } void TrackingHandlerPeaks::InitForTracking() { MITK_INFO << "Initializing peak tracker."; itk::Vector spacing4 = m_PeakImage->GetSpacing(); itk::Point origin4 = m_PeakImage->GetOrigin(); itk::Matrix direction4 = m_PeakImage->GetDirection(); itk::ImageRegion<4> imageRegion4 = m_PeakImage->GetLargestPossibleRegion(); spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2]; origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2]; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { direction3[r][c] = direction4[r][c]; m_FloatImageRotation[r][c] = direction4[r][c]; } imageRegion3.SetSize(0, imageRegion4.GetSize()[0]); imageRegion3.SetSize(1, imageRegion4.GetSize()[1]); imageRegion3.SetSize(2, imageRegion4.GetSize()[2]); m_DummyImage = ItkUcharImgType::New(); m_DummyImage->SetSpacing( spacing3 ); m_DummyImage->SetOrigin( origin3 ); m_DummyImage->SetDirection( direction3 ); m_DummyImage->SetRegions( imageRegion3 ); m_DummyImage->Allocate(); m_DummyImage->FillBuffer(0.0); m_NumDirs = imageRegion4.GetSize(3)/3; } vnl_vector_fixed TrackingHandlerPeaks::GetMatchingDirection(itk::Index<3> idx3, vnl_vector_fixed& oldDir) { vnl_vector_fixed out_dir; out_dir.fill(0); float angle = 0; float mag = oldDir.magnitude(); if (magmitk::eps) { oldDir[0] = out_dir[0]; oldDir[1] = out_dir[1]; oldDir[2] = out_dir[2]; + found = true; break; } } - // if you didn't find a non-zero random direction, take first non-zero direction you find - for (int i=0; imitk::eps) + // if you didn't find a non-zero random direction, take first non-zero direction you find + for (int i=0; imitk::eps) + { + oldDir[0] = out_dir[0]; + oldDir[1] = out_dir[1]; + oldDir[2] = out_dir[2]; + break; + } } } } else { for (int i=0; i dir = GetDirection(idx3, i); mag = dir.magnitude(); if (mag>mitk::eps) dir.normalize(); float a = dot_product(dir, oldDir); if (fabs(a)>angle) { angle = fabs(a); if (a<0) out_dir = -dir; else out_dir = dir; out_dir *= mag; out_dir *= angle; // shrink contribution of direction if is less parallel to previous direction } } } return out_dir; } vnl_vector_fixed TrackingHandlerPeaks::GetDirection(itk::Index<3> idx3, int dirIdx) { vnl_vector_fixed dir; dir.fill(0.0); if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) ) return dir; PeakImgType::IndexType idx4; idx4.SetElement(0,idx3[0]); idx4.SetElement(1,idx3[1]); idx4.SetElement(2,idx3[2]); for (int k=0; k<3; k++) { idx4.SetElement(3, dirIdx*3 + k); dir[k] = m_PeakImage->GetPixel(idx4); } if (m_FlipX) dir[0] *= -1; if (m_FlipY) dir[1] *= -1; if (m_FlipZ) dir[2] *= -1; if (m_ApplyDirectionMatrix) dir = m_FloatImageRotation*dir; return dir; } vnl_vector_fixed TrackingHandlerPeaks::GetDirection(itk::Point itkP, bool interpolate, vnl_vector_fixed oldDir){ // transform physical point to index coordinates itk::Index<3> idx3; itk::ContinuousIndex< float, 3> cIdx; m_DummyImage->TransformPhysicalPointToIndex(itkP, idx3); m_DummyImage->TransformPhysicalPointToContinuousIndex(itkP, cIdx); vnl_vector_fixed dir; dir.fill(0.0); if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) ) return dir; if (interpolate) { float frac_x = cIdx[0] - idx3[0]; float frac_y = cIdx[1] - idx3[1]; float frac_z = cIdx[2] - idx3[2]; if (frac_x<0) { idx3[0] -= 1; frac_x += 1; } if (frac_y<0) { idx3[1] -= 1; frac_y += 1; } if (frac_z<0) { idx3[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 (idx3[0] >= 0 && idx3[0] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(0) - 1) && idx3[1] >= 0 && idx3[1] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(1) - 1) && idx3[2] >= 0 && idx3[2] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(2) - 1)) { // trilinear interpolation vnl_vector_fixed interpWeights; 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); dir = GetMatchingDirection(idx3, oldDir) * interpWeights[0]; itk::Index<3> tmpIdx = idx3; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[1]; tmpIdx = idx3; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[2]; tmpIdx = idx3; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[3]; tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[4]; tmpIdx = idx3; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[5]; tmpIdx = idx3; tmpIdx[2]++; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[6]; tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[7]; } } else - dir = GetMatchingDirection(idx3, oldDir); + dir = GetMatchingDirection(idx3, oldDir); return dir; } vnl_vector_fixed TrackingHandlerPeaks::ProposeDirection(const itk::Point& pos, std::deque >& olddirs, itk::Index<3>& oldIndex) { - // CHECK: wann wird wo normalisiert + // CHECK: wann wird wo normalisiert vnl_vector_fixed output_direction; output_direction.fill(0); itk::Index<3> index; m_DummyImage->TransformPhysicalPointToIndex(pos, index); vnl_vector_fixed oldDir = olddirs.back(); float old_mag = oldDir.magnitude(); if (!m_Interpolate && oldIndex==index) return oldDir; output_direction = GetDirection(pos, m_Interpolate, oldDir); float mag = output_direction.magnitude(); if (mag>=m_PeakThreshold) { output_direction.normalize(); float a = 1; if (old_mag>0.5) - a = dot_product(output_direction, oldDir); + a = dot_product(output_direction, oldDir); if (a>m_AngularThreshold) output_direction *= mag; else output_direction.fill(0); } else output_direction.fill(0); return output_direction; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp index 3cc79f4a67..ac52889626 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp @@ -1,993 +1,992 @@ /*=================================================================== 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 #include #include #include #include "itkStreamlineTrackingFilter.h" #include #include #include #include #include "itkPointShell.h" #define _USE_MATH_DEFINES #include namespace itk { StreamlineTrackingFilter ::StreamlineTrackingFilter() : m_PauseTracking(false) , m_AbortTracking(false) , m_FiberPolyData(nullptr) , m_Points(nullptr) , m_Cells(nullptr) , m_AngularThreshold(-1) , m_StepSize(0) , m_MaxLength(10000) , m_MinTractLength(20.0) , m_MaxTractLength(400.0) , m_SeedsPerVoxel(1) , m_RandomSampling(false) , m_SamplingDistance(-1) , m_DeflectionMod(1.0) , m_OnlyForwardSamples(true) , m_UseStopVotes(true) , m_NumberOfSamples(30) , m_NumPreviousDirections(1) , m_StoppingRegions(nullptr) , m_SeedImage(nullptr) , m_MaskImage(nullptr) , m_AposterioriCurvCheck(false) , m_AvoidStop(true) , m_DemoMode(false) , m_SeedOnlyGm(false) , m_ControlGmEndings(false) , m_WmLabel(3) // mrtrix 5ttseg labels , m_GmLabel(1) // mrtrix 5ttseg labels , m_StepSizeVox(-1) , m_SamplingDistanceVox(-1) , m_AngularThresholdDeg(-1) , m_MaxNumTracts(-1) , m_Random(true) , m_Verbose(true) , m_UseOutputProbabilityMap(false) { this->SetNumberOfRequiredInputs(0); } void StreamlineTrackingFilter::BeforeTracking() { m_TrackingHandler->InitForTracking(); m_FiberPolyData = PolyDataType::New(); m_Points = vtkSmartPointer< vtkPoints >::New(); m_Cells = vtkSmartPointer< vtkCellArray >::New(); itk::Vector< double, 3 > imageSpacing = m_TrackingHandler->GetSpacing(); float minSpacing; if(imageSpacing[0]SetAngularThreshold(m_AngularThreshold); if (m_SamplingDistanceVoxGetNumberOfThreads(); i++) { PolyDataType poly = PolyDataType::New(); m_PolyDataContainer.push_back(poly); } if (m_UseOutputProbabilityMap) { m_OutputProbabilityMap = ItkDoubleImgType::New(); m_OutputProbabilityMap->SetSpacing(imageSpacing); m_OutputProbabilityMap->SetOrigin(m_TrackingHandler->GetOrigin()); m_OutputProbabilityMap->SetDirection(m_TrackingHandler->GetDirection()); m_OutputProbabilityMap->SetRegions(m_TrackingHandler->GetLargestPossibleRegion()); m_OutputProbabilityMap->Allocate(); m_OutputProbabilityMap->FillBuffer(0); } if (m_StoppingRegions.IsNull()) { m_StoppingRegions = ItkUcharImgType::New(); m_StoppingRegions->SetSpacing( imageSpacing ); m_StoppingRegions->SetOrigin( m_TrackingHandler->GetOrigin() ); m_StoppingRegions->SetDirection( m_TrackingHandler->GetDirection() ); m_StoppingRegions->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_StoppingRegions->Allocate(); m_StoppingRegions->FillBuffer(0); } else std::cout << "StreamlineTracking - Using stopping region image" << std::endl; if (m_SeedImage.IsNull()) { m_SeedImage = ItkUcharImgType::New(); m_SeedImage->SetSpacing( imageSpacing ); m_SeedImage->SetOrigin( m_TrackingHandler->GetOrigin() ); m_SeedImage->SetDirection( m_TrackingHandler->GetDirection() ); m_SeedImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_SeedImage->Allocate(); m_SeedImage->FillBuffer(1); } else std::cout << "StreamlineTracking - Using seed image" << std::endl; if (m_MaskImage.IsNull()) { // initialize mask image m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( imageSpacing ); m_MaskImage->SetOrigin( m_TrackingHandler->GetOrigin() ); m_MaskImage->SetDirection( m_TrackingHandler->GetDirection() ); m_MaskImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } else std::cout << "StreamlineTracking - Using mask image" << std::endl; if (m_SeedPoints.empty()) GetSeedPointsFromSeedImage(); else m_SeedOnlyGm = false; if (m_TissueImage.IsNull()) { if (m_SeedOnlyGm) { MITK_WARN << "StreamlineTracking - Cannot seed in gray matter. No tissue type image set."; m_SeedOnlyGm = false; } if (m_ControlGmEndings) { MITK_WARN << "StreamlineTracking - Cannot control gray matter endings. No tissue type image set."; m_ControlGmEndings = false; } } else { if (m_ControlGmEndings) m_SeedOnlyGm = true; if (m_ControlGmEndings || m_SeedOnlyGm) std::cout << "StreamlineTracking - Using tissue image" << std::endl; else MITK_WARN << "StreamlineTracking - Tissue image set but no gray matter seeding or fiber endpoint-control enabled" << std::endl; } m_BuildFibersReady = 0; m_BuildFibersFinished = false; m_Tractogram.clear(); m_SamplingPointset = mitk::PointSet::New(); m_AlternativePointset = mitk::PointSet::New(); m_StopVotePointset = mitk::PointSet::New(); m_StartTime = std::chrono::system_clock::now(); if (m_SeedOnlyGm && m_ControlGmEndings) InitGrayMatterEndings(); if (m_DemoMode) omp_set_num_threads(1); - omp_set_num_threads(1); if (m_TrackingHandler->GetMode()==mitk::TrackingDataHandler::MODE::DETERMINISTIC) std::cout << "StreamlineTracking - Mode: deterministic" << std::endl; else if(m_TrackingHandler->GetMode()==mitk::TrackingDataHandler::MODE::PROBABILISTIC) std::cout << "StreamlineTracking - Mode: probabilistic" << std::endl; else std::cout << "StreamlineTracking - Mode: ???" << std::endl; std::cout << "StreamlineTracking - Angular threshold: " << m_AngularThreshold << " (" << 180*std::acos( m_AngularThreshold )/M_PI << "°)" << std::endl; std::cout << "StreamlineTracking - Stepsize: " << m_StepSize << "mm (" << m_StepSize/minSpacing << "*vox)" << std::endl; std::cout << "StreamlineTracking - Seeds per voxel: " << m_SeedsPerVoxel << std::endl; std::cout << "StreamlineTracking - Max. tract length: " << m_MaxTractLength << "mm" << std::endl; std::cout << "StreamlineTracking - Min. tract length: " << m_MinTractLength << "mm" << std::endl; std::cout << "StreamlineTracking - Max. num. tracts: " << m_MaxNumTracts << std::endl; std::cout << "StreamlineTracking - Num. neighborhood samples: " << m_NumberOfSamples << std::endl; std::cout << "StreamlineTracking - Max. sampling distance: " << m_SamplingDistance << "mm (" << m_SamplingDistance/minSpacing << "*vox)" << std::endl; std::cout << "StreamlineTracking - Deflection modifier: " << m_DeflectionMod << std::endl; std::cout << "StreamlineTracking - Use stop votes: " << m_UseStopVotes << std::endl; std::cout << "StreamlineTracking - Only frontal samples: " << m_OnlyForwardSamples << std::endl; if (m_DemoMode) { std::cout << "StreamlineTracking - Running in demo mode"; std::cout << "StreamlineTracking - Starting streamline tracking using 1 thread" << std::endl; } else std::cout << "StreamlineTracking - Starting streamline tracking using " << omp_get_max_threads() << " threads" << std::endl; } void StreamlineTrackingFilter::InitGrayMatterEndings() { m_TrackingHandler->SetAngularThreshold(0); m_GmStubs.clear(); if (m_TissueImage.IsNotNull()) { std::cout << "StreamlineTracking - initializing GM endings" << std::endl; ImageRegionConstIterator< ItkUcharImgType > it(m_TissueImage, m_TissueImage->GetLargestPossibleRegion() ); it.GoToBegin(); vnl_vector_fixed d1; d1.fill(0.0); std::deque< vnl_vector_fixed > olddirs; while (olddirs.size() start; m_TissueImage->TransformIndexToPhysicalPoint(s_idx, start); itk::Point wm_p; float max = -1; FiberType fib; for (int x : {-1,0,1}) for (int y : {-1,0,1}) for (int z : {-1,0,1}) { if (x==y && y==z) continue; ItkUcharImgType::IndexType e_idx; e_idx[0] = s_idx[0] + x; e_idx[1] = s_idx[1] + y; e_idx[2] = s_idx[2] + z; if ( !m_TissueImage->GetLargestPossibleRegion().IsInside(e_idx) || m_TissueImage->GetPixel(e_idx)!=m_WmLabel ) continue; itk::ContinuousIndex end; m_TissueImage->TransformIndexToPhysicalPoint(e_idx, end); d1 = m_TrackingHandler->ProposeDirection(end, olddirs, s_idx); if (d1.magnitude()<0.0001) continue; d1.normalize(); vnl_vector_fixed< float, 3 > d2; d2[0] = end[0] - start[0]; d2[1] = end[1] - start[1]; d2[2] = end[2] - start[2]; d2.normalize(); float a = fabs(dot_product(d1,d2)); if (a>max) { max = a; wm_p = end; } } if (max>=0) { fib.push_back(start); fib.push_back(wm_p); m_GmStubs.push_back(fib); } } ++it; } } m_TrackingHandler->SetAngularThreshold(m_AngularThreshold); } void StreamlineTrackingFilter::CalculateNewPosition(itk::Point& pos, vnl_vector_fixed& dir) { pos[0] += dir[0]*m_StepSize; pos[1] += dir[1]*m_StepSize; pos[2] += dir[2]*m_StepSize; } bool StreamlineTrackingFilter ::IsValidPosition(const itk::Point &pos) { ItkUcharImgType::IndexType idx; m_MaskImage->TransformPhysicalPointToIndex(pos, idx); if (!m_MaskImage->GetLargestPossibleRegion().IsInside(idx) || m_MaskImage->GetPixel(idx)==0) return false; return true; } bool StreamlineTrackingFilter ::IsInGm(const itk::Point &pos) { if (m_TissueImage.IsNull()) return true; ItkUcharImgType::IndexType idx; m_TissueImage->TransformPhysicalPointToIndex(pos, idx); if (m_TissueImage->GetLargestPossibleRegion().IsInside(idx) && m_TissueImage->GetPixel(idx) == m_GmLabel) return true; return false; } float StreamlineTrackingFilter::GetRandDouble(float min, float max) { return (float)(rand()%((int)(10000*(max-min))) + 10000*min)/10000; } std::vector< vnl_vector_fixed > StreamlineTrackingFilter::CreateDirections(int NPoints) { std::vector< vnl_vector_fixed > pointshell; if (NPoints<2) return pointshell; std::vector< float > theta; theta.resize(NPoints); std::vector< float > phi; phi.resize(NPoints); float C = sqrt(4*M_PI); phi[0] = 0.0; phi[NPoints-1] = 0.0; for(int i=0; i0 && i d; d[0] = cos(theta[i]) * cos(phi[i]); d[1] = cos(theta[i]) * sin(phi[i]); d[2] = sin(theta[i]); pointshell.push_back(d); } return pointshell; } vnl_vector_fixed StreamlineTrackingFilter::GetNewDirection(itk::Point &pos, std::deque >& olddirs, itk::Index<3> &oldIndex) { if (m_DemoMode) { m_SamplingPointset->Clear(); m_AlternativePointset->Clear(); m_StopVotePointset->Clear(); } vnl_vector_fixed direction; direction.fill(0); ItkUcharImgType::IndexType idx; m_MaskImage->TransformPhysicalPointToIndex(pos, idx); if (IsValidPosition(pos)) { if (m_StoppingRegions->GetPixel(idx)>0) return direction; direction = m_TrackingHandler->ProposeDirection(pos, olddirs, oldIndex); // get direction proposal at current streamline position } else return direction; vnl_vector_fixed olddir = olddirs.back(); std::vector< vnl_vector_fixed > probeVecs = CreateDirections(m_NumberOfSamples); itk::Point sample_pos; int alternatives = 1; int stop_votes = 0; int possible_stop_votes = 0; for (int i=0; i d; bool is_stop_voter = false; if (m_RandomSampling) { d[0] = GetRandDouble(); d[1] = GetRandDouble(); d[2] = GetRandDouble(); d.normalize(); d *= GetRandDouble(0,m_SamplingDistance); } else { d = probeVecs.at(i); float dot = dot_product(d, olddir); if (m_UseStopVotes && dot>0.7) { is_stop_voter = true; possible_stop_votes++; } else if (m_OnlyForwardSamples && dot<0) continue; d *= m_SamplingDistance; } sample_pos[0] = pos[0] + d[0]; sample_pos[1] = pos[1] + d[1]; sample_pos[2] = pos[2] + d[2]; vnl_vector_fixed tempDir; tempDir.fill(0.0); if (IsValidPosition(sample_pos)) tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood if (tempDir.magnitude()>mitk::eps) { direction += tempDir; if(m_DemoMode) m_SamplingPointset->InsertPoint(i, sample_pos); } else if (m_AvoidStop && olddir.magnitude()>0.5) // out of white matter { if (is_stop_voter) stop_votes++; if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); float dot = dot_product(d, olddir); if (dot >= 0.0) // in front of plane defined by pos and olddir d = -d + 2*dot*olddir; // reflect else d = -d; // invert // look a bit further into the other direction sample_pos[0] = pos[0] + d[0]; sample_pos[1] = pos[1] + d[1]; sample_pos[2] = pos[2] + d[2]; alternatives++; vnl_vector_fixed tempDir; tempDir.fill(0.0); if (IsValidPosition(sample_pos)) tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood if (tempDir.magnitude()>mitk::eps) // are we back in the white matter? { direction += d * m_DeflectionMod; // go into the direction of the white matter direction += tempDir; // go into the direction of the white matter direction at this location if(m_DemoMode) m_AlternativePointset->InsertPoint(alternatives, sample_pos); } else { if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); } } else { if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); if (is_stop_voter) stop_votes++; } } if (direction.magnitude()>0.001 && (possible_stop_votes==0 || (float)stop_votes/possible_stop_votes<0.5) ) direction.normalize(); else direction.fill(0); return direction; } float StreamlineTrackingFilter::FollowStreamline(itk::Point pos, vnl_vector_fixed dir, FiberType* fib, float tractLength, bool front) { vnl_vector_fixed zero_dir; zero_dir.fill(0.0); std::deque< vnl_vector_fixed > last_dirs; for (unsigned int i=0; iTransformPhysicalPointToIndex(pos, oldIndex); // get new position CalculateNewPosition(pos, dir); // is new position inside of image and mask if (m_AbortTracking) // if not end streamline { return tractLength; } else // if yes, add new point to streamline { tractLength += m_StepSize; if (front) fib->push_front(pos); else fib->push_back(pos); if (m_AposterioriCurvCheck) { int curv = CheckCurvature(fib, front); if (curv>0) { tractLength -= m_StepSize*curv; while (curv>0) { if (front) fib->pop_front(); else fib->pop_back(); curv--; } return tractLength; } } if (tractLength>m_MaxTractLength) return tractLength; } #pragma omp critical if (m_DemoMode && !m_UseOutputProbabilityMap) // CHECK: warum sind die samplingpunkte der streamline in der visualisierung immer einen schritt voras? { m_BuildFibersReady++; m_Tractogram.push_back(*fib); BuildFibers(true); m_Stop = true; while (m_Stop){ } } dir.normalize(); last_dirs.push_back(dir); if (last_dirs.size()>m_NumPreviousDirections) last_dirs.pop_front(); dir = GetNewDirection(pos, last_dirs, oldIndex); while (m_PauseTracking){} if (dir.magnitude()<0.0001) return tractLength; } return tractLength; } int StreamlineTrackingFilter::CheckCurvature(FiberType* fib, bool front) { float m_Distance = 5; if (fib->size()<3) return 0; float dist = 0; std::vector< vnl_vector_fixed< float, 3 > > vectors; vnl_vector_fixed< float, 3 > meanV; meanV.fill(0); float dev = 0; if (front) { int c=0; while(distsize()-1) { itk::Point p1 = fib->at(c); itk::Point p2 = fib->at(c+1); vnl_vector_fixed< float, 3 > v; v[0] = p2[0]-p1[0]; v[1] = p2[1]-p1[1]; v[2] = p2[2]-p1[2]; dist += v.magnitude(); v.normalize(); vectors.push_back(v); if (c==0) meanV += v; c++; } } else { int c=fib->size()-1; while(dist0) { itk::Point p1 = fib->at(c); itk::Point p2 = fib->at(c-1); vnl_vector_fixed< float, 3 > v; v[0] = p2[0]-p1[0]; v[1] = p2[1]-p1[1]; v[2] = p2[2]-p1[2]; dist += v.magnitude(); v.normalize(); vectors.push_back(v); if (c==fib->size()-1) meanV += v; c--; } } meanV.normalize(); for (int c=0; c1.0) angle = 1.0; if (angle<-1.0) angle = -1.0; dev += acos(angle)*180/M_PI; } if (vectors.size()>0) dev /= vectors.size(); if (dev<30) return 0; else return vectors.size(); } void StreamlineTrackingFilter::GetSeedPointsFromSeedImage() { MITK_INFO << "Calculating seed points."; m_SeedPoints.clear(); if (!m_ControlGmEndings) { typedef ImageRegionConstIterator< ItkUcharImgType > MaskIteratorType; MaskIteratorType sit(m_SeedImage, m_SeedImage->GetLargestPossibleRegion()); sit.GoToBegin(); while (!sit.IsAtEnd()) { if (sit.Value()>0) { ItkUcharImgType::IndexType index = sit.GetIndex(); itk::ContinuousIndex start; start[0] = index[0]; start[1] = index[1]; start[2] = index[2]; itk::Point worldPos; m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos); if (IsValidPosition(worldPos) && (!m_SeedOnlyGm || IsInGm(worldPos))) { m_SeedPoints.push_back(worldPos); for (int s = 1; s < m_SeedsPerVoxel; s++) { start[0] = index[0] + GetRandDouble(-0.5, 0.5); start[1] = index[1] + GetRandDouble(-0.5, 0.5); start[2] = index[2] + GetRandDouble(-0.5, 0.5); itk::Point worldPos; m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos); m_SeedPoints.push_back(worldPos); } } } ++sit; } } else { for (auto s : m_GmStubs) m_SeedPoints.push_back(s[1]); } } void StreamlineTrackingFilter::GenerateData() { this->BeforeTracking(); if (m_Random) { std::srand(std::time(0)); std::random_shuffle(m_SeedPoints.begin(), m_SeedPoints.end()); } bool stop = false; unsigned int current_tracts = 0; int num_seeds = m_SeedPoints.size(); itk::Index<3> zeroIndex; zeroIndex.Fill(0); int progress = 0; int i = 0; int print_interval = num_seeds/100; if (print_interval<100) m_Verbose=false; #pragma omp parallel while (i=num_seeds || stop) continue; else if (m_Verbose && i%print_interval==0) #pragma omp critical { progress += print_interval; std::cout << " \r"; if (m_MaxNumTracts>0) std::cout << "Tried: " << progress << "/" << num_seeds << " | Accepted: " << current_tracts << "/" << m_MaxNumTracts << '\r'; else std::cout << "Tried: " << progress << "/" << num_seeds << " | Accepted: " << current_tracts << '\r'; cout.flush(); } const itk::Point worldPos = m_SeedPoints.at(temp_i); FiberType fib; float tractLength = 0; unsigned int counter = 0; // get starting direction vnl_vector_fixed dir; dir.fill(0.0); std::deque< vnl_vector_fixed > olddirs; while (olddirs.size() gm_start_dir; if (m_ControlGmEndings) { gm_start_dir[0] = m_GmStubs[temp_i][1][0] - m_GmStubs[temp_i][0][0]; gm_start_dir[1] = m_GmStubs[temp_i][1][1] - m_GmStubs[temp_i][0][1]; gm_start_dir[2] = m_GmStubs[temp_i][1][2] - m_GmStubs[temp_i][0][2]; gm_start_dir.normalize(); olddirs.pop_back(); olddirs.push_back(gm_start_dir); } if (IsValidPosition(worldPos)) dir = m_TrackingHandler->ProposeDirection(worldPos, olddirs, zeroIndex); if (dir.magnitude()>0.0001) { if (m_ControlGmEndings) { float a = dot_product(gm_start_dir, dir); if (a<0) dir = -dir; } // forward tracking tractLength = FollowStreamline(worldPos, dir, &fib, 0, false); fib.push_front(worldPos); if (m_ControlGmEndings) { fib.push_front(m_GmStubs[temp_i][0]); CheckFiberForGmEnding(&fib); } else { // backward tracking (only if we don't explicitely start in the GM) tractLength = FollowStreamline(worldPos, -dir, &fib, tractLength, true); if (m_ControlGmEndings) { CheckFiberForGmEnding(&fib); std::reverse(fib.begin(),fib.end()); CheckFiberForGmEnding(&fib); } } counter = fib.size(); #pragma omp critical if (tractLength>=m_MinTractLength && counter>=2) { if (!stop) { if (!m_UseOutputProbabilityMap) m_Tractogram.push_back(fib); else FiberToProbmap(&fib); current_tracts++; } if (m_MaxNumTracts > 0 && current_tracts>=static_cast(m_MaxNumTracts)) { if (!stop) { std::cout << " \r"; MITK_INFO << "Reconstructed maximum number of tracts (" << current_tracts << "). Stopping tractography."; } stop = true; } } } } this->AfterTracking(); } void StreamlineTrackingFilter::CheckFiberForGmEnding(FiberType* fib) { if (m_TissueImage.IsNull()) return; // first check if the current fibe rendpoint is located inside of the white matter // if not, remove last fiber point and repeat bool in_wm = false; while (!in_wm && fib->size()>2) { ItkUcharImgType::IndexType idx; m_TissueImage->TransformPhysicalPointToIndex(fib->back(), idx); if (m_TissueImage->GetPixel(idx)==m_WmLabel) in_wm = true; else fib->pop_back(); } if (fib->size()<3 || !in_wm) { fib->clear(); return; } // get fiber direction at end point vnl_vector_fixed< float, 3 > d1; d1[0] = fib->back()[0] - fib->at(fib->size()-2)[0]; d1[1] = fib->back()[1] - fib->at(fib->size()-2)[1]; d1[2] = fib->back()[2] - fib->at(fib->size()-2)[2]; d1.normalize(); // find closest gray matter voxel ItkUcharImgType::IndexType s_idx; m_TissueImage->TransformPhysicalPointToIndex(fib->back(), s_idx); itk::Point gm_endp; float max = -1; for (int x : {-1,0,1}) for (int y : {-1,0,1}) for (int z : {-1,0,1}) { if (x==y && y==z) continue; ItkUcharImgType::IndexType e_idx; e_idx[0] = s_idx[0] + x; e_idx[1] = s_idx[1] + y; e_idx[2] = s_idx[2] + z; if ( !m_TissueImage->GetLargestPossibleRegion().IsInside(e_idx) || m_TissueImage->GetPixel(e_idx)!=m_GmLabel ) continue; itk::ContinuousIndex end; m_TissueImage->TransformIndexToPhysicalPoint(e_idx, end); vnl_vector_fixed< float, 3 > d2; d2[0] = end[0] - fib->back()[0]; d2[1] = end[1] - fib->back()[1]; d2[2] = end[2] - fib->back()[2]; d2.normalize(); float a = dot_product(d1,d2); if (a>max) { max = a; gm_endp = end; } } if (max>=0) fib->push_back(gm_endp); else // no gray matter enpoint found -> delete fiber fib->clear(); } void StreamlineTrackingFilter::FiberToProbmap(FiberType* fib) { ItkDoubleImgType::IndexType last_idx; last_idx.Fill(0); for (auto p : *fib) { ItkDoubleImgType::IndexType idx; m_OutputProbabilityMap->TransformPhysicalPointToIndex(p, idx); if (idx != last_idx) { if (m_OutputProbabilityMap->GetLargestPossibleRegion().IsInside(idx)) m_OutputProbabilityMap->SetPixel(idx, m_OutputProbabilityMap->GetPixel(idx)+1); last_idx = idx; } } } void StreamlineTrackingFilter::BuildFibers(bool check) { if (m_BuildFibersReady::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); for (int i=0; i container = vtkSmartPointer::New(); FiberType fib = m_Tractogram.at(i); for (FiberType::iterator it = fib.begin(); it!=fib.end(); ++it) { vtkIdType id = vNewPoints->InsertNextPoint((*it).GetDataPointer()); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } if (check) for (int i=0; iSetPoints(vNewPoints); m_FiberPolyData->SetLines(vNewLines); m_BuildFibersFinished = true; } void StreamlineTrackingFilter::AfterTracking() { if (m_Verbose) std::cout << " \r"; if (!m_UseOutputProbabilityMap) { MITK_INFO << "Reconstructed " << m_Tractogram.size() << " fibers."; MITK_INFO << "Generating polydata "; BuildFibers(false); } MITK_INFO << "done"; m_EndTime = std::chrono::system_clock::now(); std::chrono::hours hh = std::chrono::duration_cast(m_EndTime - m_StartTime); std::chrono::minutes mm = std::chrono::duration_cast(m_EndTime - m_StartTime); std::chrono::seconds ss = std::chrono::duration_cast(m_EndTime - m_StartTime); mm %= 60; ss %= 60; MITK_INFO << "Tracking took " << hh.count() << "h, " << mm.count() << "m and " << ss.count() << "s"; m_SeedPoints.clear(); } } diff --git a/Modules/DiffusionImaging/cmdapps/RfTraining.cpp b/Modules/DiffusionImaging/cmdapps/RfTraining.cpp index ebda300334..fd209045b8 100755 --- a/Modules/DiffusionImaging/cmdapps/RfTraining.cpp +++ b/Modules/DiffusionImaging/cmdapps/RfTraining.cpp @@ -1,228 +1,228 @@ /*=================================================================== 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 #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include using namespace std; /*! \brief Train random forest classifier for machine learning based streamline tractography */ int main(int argc, char* argv[]) { MITK_INFO << "RfTraining"; mitkCommandLineParser parser; - parser.setTitle("Training for Machine Learning Based Streamline Tractography"); + parser.setTitle("Trains Random Forests for Machine Learning Based Tractography"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription("Train random forest classifier for machine learning based streamline tractography"); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("images", "i", mitkCommandLineParser::StringList, "DWIs:", "input diffusion-weighted images", us::Any(), false); parser.addArgument("tractograms", "t", mitkCommandLineParser::StringList, "Tractograms:", "input training tractograms (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("forest", "f", mitkCommandLineParser::OutputFile, "Forest:", "output random forest (HDF5)", us::Any(), false); parser.addArgument("masks", "", mitkCommandLineParser::StringList, "Masks:", "restrict training using a binary mask image", us::Any()); parser.addArgument("wm_masks", "", mitkCommandLineParser::StringList, "WM-Masks:", "if no binary white matter mask is specified, the envelope of the input tractogram is used", us::Any()); parser.addArgument("volume_modification_images", "", mitkCommandLineParser::StringList, "Volume modification images:", "specify a list of float images that modify the fiber density", us::Any()); parser.addArgument("additional_feature_images", "", mitkCommandLineParser::StringList, "Additional feature images:", "specify a list of float images that hold additional features (float)", us::Any()); parser.addArgument("sampling_distance", "", mitkCommandLineParser::Float, "Sampling distance:", "resampling parameter for the input tractogram in mm (determines number of white-matter samples)", us::Any()); parser.addArgument("num_gm_samples", "", mitkCommandLineParser::Int, "Number of gray matter samples per voxel:", "Number of gray matter samples per voxel", us::Any()); parser.addArgument("num_trees", "", mitkCommandLineParser::Int, "Number of trees:", "number of trees", 30); parser.addArgument("max_tree_depth", "", mitkCommandLineParser::Int, "Max. tree depth:", "maximum tree depth", 25); parser.addArgument("sample_fraction", "", mitkCommandLineParser::Float, "Sample fraction:", "fraction of samples used per tree", 0.7); parser.addArgument("use_sh_features", "", mitkCommandLineParser::Bool, "Use SH features:", "use SH features", false); parser.addArgument("max_wm_samples", "", mitkCommandLineParser::Int, "Max. num. WM samples:", "upper limit for the number of WM samples"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; bool shfeatures = false; if (parsedArgs.count("use_sh_features")) shfeatures = us::any_cast(parsedArgs["use_sh_features"]); mitkCommandLineParser::StringContainerType imageFiles = us::any_cast(parsedArgs["images"]); mitkCommandLineParser::StringContainerType wmMaskFiles; if (parsedArgs.count("wm_masks")) wmMaskFiles = us::any_cast(parsedArgs["wm_masks"]); mitkCommandLineParser::StringContainerType volModFiles; if (parsedArgs.count("volume_modification_images")) volModFiles = us::any_cast(parsedArgs["volume_modification_images"]); mitkCommandLineParser::StringContainerType addFeatFiles; if (parsedArgs.count("additional_feature_images")) addFeatFiles = us::any_cast(parsedArgs["additional_feature_images"]); mitkCommandLineParser::StringContainerType maskFiles; if (parsedArgs.count("masks")) maskFiles = us::any_cast(parsedArgs["masks"]); string forestFile = us::any_cast(parsedArgs["forest"]); mitkCommandLineParser::StringContainerType tractogramFiles; if (parsedArgs.count("tractograms")) tractogramFiles = us::any_cast(parsedArgs["tractograms"]); int num_trees = 30; if (parsedArgs.count("num_trees")) num_trees = us::any_cast(parsedArgs["num_trees"]); int gm_samples = -1; if (parsedArgs.count("num_gm_samples")) gm_samples = us::any_cast(parsedArgs["num_gm_samples"]); float sampling_distance = -1; if (parsedArgs.count("sampling_distance")) sampling_distance = us::any_cast(parsedArgs["sampling_distance"]); int max_tree_depth = 25; if (parsedArgs.count("max_tree_depth")) max_tree_depth = us::any_cast(parsedArgs["max_tree_depth"]); double sample_fraction = 0.7; if (parsedArgs.count("sample_fraction")) sample_fraction = us::any_cast(parsedArgs["sample_fraction"]); int maxWmSamples = -1; if (parsedArgs.count("max_wm_samples")) maxWmSamples = us::any_cast(parsedArgs["max_wm_samples"]); MITK_INFO << "loading diffusion-weighted images"; std::vector< mitk::Image::Pointer > rawData; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {}); for (auto imgFile : imageFiles) { mitk::Image::Pointer dwi = dynamic_cast(mitk::IOUtil::LoadImage(imgFile, &functor).GetPointer()); rawData.push_back(dwi); } typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; MITK_INFO << "loading mask images"; std::vector< ItkUcharImgType::Pointer > maskImageVector; for (auto maskFile : maskFiles) { mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadImage(maskFile).GetPointer()); ItkUcharImgType::Pointer mask = ItkUcharImgType::New(); mitk::CastToItkImage(img, mask); maskImageVector.push_back(mask); } MITK_INFO << "loading white matter mask images"; std::vector< ItkUcharImgType::Pointer > wmMaskImageVector; for (auto wmFile : wmMaskFiles) { mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadImage(wmFile).GetPointer()); ItkUcharImgType::Pointer wmmask = ItkUcharImgType::New(); mitk::CastToItkImage(img, wmmask); wmMaskImageVector.push_back(wmmask); } MITK_INFO << "loading tractograms"; std::vector< mitk::FiberBundle::Pointer > tractograms; for (auto tractFile : tractogramFiles) { mitk::FiberBundle::Pointer fib = dynamic_cast(mitk::IOUtil::Load(tractFile).at(0).GetPointer()); tractograms.push_back(fib); } MITK_INFO << "loading white volume modification images"; std::vector< ItkFloatImgType::Pointer > volumeModImages; for (auto file : volModFiles) { mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadImage(file).GetPointer()); ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New(); mitk::CastToItkImage(img, itkimg); volumeModImages.push_back(itkimg); } MITK_INFO << "loading additional feature images"; std::vector< std::vector< ItkFloatImgType::Pointer > > addFeatImages; for (int i=0; i()); int c = 0; for (auto file : addFeatFiles) { mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadImage(file).GetPointer()); ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New(); mitk::CastToItkImage(img, itkimg); addFeatImages.at(c%addFeatImages.size()).push_back(itkimg); c++; } if (shfeatures) { mitk::TrackingHandlerRandomForest<6,28> forestHandler; forestHandler.SetDwis(rawData); forestHandler.SetMaskImages(maskImageVector); forestHandler.SetWhiteMatterImages(wmMaskImageVector); forestHandler.SetFiberVolumeModImages(volumeModImages); forestHandler.SetAdditionalFeatureImages(addFeatImages); forestHandler.SetTractograms(tractograms); forestHandler.SetNumTrees(num_trees); forestHandler.SetMaxTreeDepth(max_tree_depth); forestHandler.SetGrayMatterSamplesPerVoxel(gm_samples); forestHandler.SetSampleFraction(sample_fraction); forestHandler.SetStepSize(sampling_distance); forestHandler.SetMaxNumWmSamples(maxWmSamples); forestHandler.StartTraining(); forestHandler.SaveForest(forestFile); } else { mitk::TrackingHandlerRandomForest<6,100> forestHandler; forestHandler.SetDwis(rawData); forestHandler.SetMaskImages(maskImageVector); forestHandler.SetWhiteMatterImages(wmMaskImageVector); forestHandler.SetFiberVolumeModImages(volumeModImages); forestHandler.SetAdditionalFeatureImages(addFeatImages); forestHandler.SetTractograms(tractograms); forestHandler.SetNumTrees(num_trees); forestHandler.SetMaxTreeDepth(max_tree_depth); forestHandler.SetGrayMatterSamplesPerVoxel(gm_samples); forestHandler.SetSampleFraction(sample_fraction); forestHandler.SetStepSize(sampling_distance); forestHandler.SetMaxNumWmSamples(maxWmSamples); forestHandler.StartTraining(); forestHandler.SaveForest(forestFile); } return EXIT_SUCCESS; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake index f474bd302f..cb08f4f6c7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake @@ -1,60 +1,65 @@ set(SRC_CPP_FILES QmitkFreeSurferParcellationHandler.cpp QmitkFreeSurferParcellationWidget.cpp ) set(INTERNAL_CPP_FILES QmitkConnectomicsDataView.cpp QmitkConnectomicsNetworkOperationsView.cpp QmitkConnectomicsStatisticsView.cpp QmitkNetworkHistogramCanvas.cpp QmitkRandomParcellationView.cpp + Perspectives/QmitkConnectomicsPerspective.cpp + mitkPluginActivator.cpp ) set(UI_FILES src/internal/QmitkConnectomicsDataViewControls.ui src/internal/QmitkConnectomicsNetworkOperationsViewControls.ui src/internal/QmitkConnectomicsStatisticsViewControls.ui src/internal/QmitkRandomParcellationViewControls.ui src/QmitkFreeSurferParcellationWidgetControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h + src/internal/Perspectives/QmitkConnectomicsPerspective.h + src/internal/QmitkConnectomicsDataView.h src/internal/QmitkConnectomicsNetworkOperationsView.h src/internal/QmitkConnectomicsStatisticsView.h src/internal/QmitkNetworkHistogramCanvas.h src/internal/QmitkRandomParcellationView.h src/QmitkFreeSurferParcellationHandler.h src/QmitkFreeSurferParcellationWidget.h ) set(CACHED_RESOURCE_FILES plugin.xml resources/QmitkConnectomicsDataViewIcon_48.png resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png resources/QmitkConnectomicsStatisticsViewIcon_48.png resources/QmitkRandomParcellationIcon.png + resources/parcellation.png ) set(QRC_FILES resources/QmitkDiffusionImaging.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml index 3bd47d3286..5fb49abd47 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml @@ -1,41 +1,53 @@ + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png new file mode 100644 index 0000000000..3469f6c9d4 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp similarity index 81% copy from Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp copy to Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp index 70c55d4280..41d242cb19 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp @@ -1,50 +1,47 @@ /*=================================================================== 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 "QmitkDIAppIVIMPerspective.h" +#include "QmitkConnectomicsPerspective.h" #include "berryIViewLayout.h" -void QmitkDIAppIVIMPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) +void QmitkConnectomicsPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// - left->AddView("org.mitk.views.ivim"); - berry::IViewLayout::Pointer lo = layout->GetViewLayout("org.mitk.views.ivim"); - - - left->AddView("org.mitk.views.segmentation"); - lo = layout->GetViewLayout("org.mitk.views.segmentation"); - + left->AddView("org.mitk.views.connectomicsdata"); + left->AddView("org.mitk.views.connectomicsstatistics"); + left->AddView("org.mitk.views.connectomicsnetworkoperations"); + left->AddView("org.mitk.views.randomparcellationview"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h new file mode 100644 index 0000000000..9060b0185c --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h @@ -0,0 +1,36 @@ +/*=================================================================== + +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 QmitkConnectomicsPerspective_H_ +#define QmitkConnectomicsPerspective_H_ + +#include + +class QmitkConnectomicsPerspective : public QObject, public berry::IPerspectiveFactory +{ + Q_OBJECT + Q_INTERFACES(berry::IPerspectiveFactory) + +public: + + QmitkConnectomicsPerspective() {} + ~QmitkConnectomicsPerspective() {} + + void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; +}; + +#endif /* QmitkConnectomicsPerspective_H_ */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp index d3cf66a9e3..28913b3601 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp @@ -1,44 +1,47 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include "src/internal/QmitkConnectomicsDataView.h" #include "src/internal/QmitkConnectomicsNetworkOperationsView.h" #include "src/internal/QmitkConnectomicsStatisticsView.h" #include "src/internal/QmitkRandomParcellationView.h" +#include "src/internal/Perspectives/QmitkConnectomicsPerspective.h" ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { + BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsPerspective, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsDataView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsNetworkOperationsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkRandomParcellationView, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui index 4ee765fa3e..3166f3c7a3 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3447 +1,3447 @@ QmitkFiberfoxViewControls 0 0 524 2652 Form Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico - 0 + 1 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 :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Operations false Join Bundles :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. 3 -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. 3 -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. 3 -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false Transform Selection :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico 32 32 false true Qt::Horizontal 40 20 Signal Generation Extra-axonal Compartments QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Prototype Signal Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Prototype Signal Qt::Vertical 20 40 Image Settings Advanced Options QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 <html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html> false b-value in s/mm² 0 10000 100 1000 color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p>Number of Channels:</p></body></html> false TR in milliseconds 1 999999999 1 4000 Output one image per compartment containing the corresponding volume fractions per voxel. Reverse Phase Encoding Direction false Signal Scale: Dwell time (time to read one line in k-space) in ms. 100.000000000000000 0.100000000000000 1.000000000000000 TE in milliseconds 1 999999999 1 100 Fiber Radius: Partial Fourier: false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false <html><head/><body><p>Coil Sensitivity:</p></body></html> false Partial fourier factor (0.5-1) 3 0.500000000000000 1.000000000000000 0.100000000000000 1.000000000000000 Output phase image and volume fraction maps. Output Additional Images false Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 <html><head/><body><p>Repetition Time <span style=" font-style:italic;">TR</span>: </p></body></html> false Constant Linear Exponential Dwell Time: false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false TE in milliseconds 1 10000 1 100 Number of coil elements used for the acquisiton. 1 128 1 1 Acquisition Type: Single Shot EPI Spin Echo Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 9999.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 20 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 20 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Data QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - ... <html><head/><body><p>Select a binary image to define the area of signal generation. Outside of the mask image only noise will be actively generated.</p></body></html> QComboBox::AdjustToMinimumContentsLength Fiber Bundle: false Save path: false Tissue Mask: false <html><head/><body><p>Select a fiber bundle to generate the white matter signal from. You can either use the fiber definition tab to manually define an input fiber bundle or you can also use any existing bundle, e.g. yielded by a tractography algorithm.</p></body></html> QComboBox::AdjustToMinimumContentsLength Template Image: false <html><head/><body><p>The parameters for the simulation (e.g. spacing, size, diffuison-weighted gradients, b-value) are adopted from this image.</p></body></html> QComboBox::AdjustToMinimumContentsLength 8 true Noise and other Artifacts Add Distortions false Add Spikes false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Gradient: false Eddy current induced magnetic field gradient (in mT/m). 4 1000.000000000000000 0.001000000000000 0.010000000000000 Add Motion Artifacts false Qt::Horizontal true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 Add Noise false QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: true QFrame::NoFrame QFrame::Raised 0 6 0 0 6 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 Degree: false x false Axis: false Maximum rotation around x-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 0.000000000000000 Maximum rotation around z-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 15.000000000000000 y false z false Maximum rotation around y-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 0.000000000000000 Translation 0 0 0 Distance: false x false y false Axis: false z false Maximum translation along x-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along y-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along z-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Motion volumes: Type in the volume indices that should be affected by motion (e.g. "0 3 7" whithout quotation marks). Leave blank for motion in all volumes. Type in "random" to randomly select volumes for motion. A list of negative numbers (e.g. -1 -2 -3) excludes volumes (e.g. 1 2 3) selects all remaining volumes. random Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Qt::Horizontal Qt::Horizontal Qt::Horizontal Qt::Horizontal Add N/2 Ghosts false Add Aliasing false Qt::Horizontal Qt::Horizontal Add Eddy Current Effects false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 25.000000000000000 true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 10 0.000000000000000 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Complex Gaussian Rician true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Start Simulation :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model Prototype Signal QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico + + QmitkDataStorageComboBoxWithSelectNone + QComboBox +
QmitkDataStorageComboBoxWithSelectNone.h
+ QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 QmitkPrototypeSignalParametersWidget QWidget
QmitkPrototypeSignalParametersWidget.h
1 - - QmitkDataStorageComboBoxWithSelectNone - QComboBox -
QmitkDataStorageComboBoxWithSelectNone.h
- m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_FiberBundleComboBox m_MaskComboBox m_TemplateComboBox m_SavePathEdit m_OutputPathButton m_GenerateImageButton m_AbortSimulationButton m_SimulationStatusText m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_SignalScaleBox m_TEbox m_TRbox m_LineReadoutTimeBox m_PartialFourier m_T2starBox m_FiberRadius m_ReversePhaseBox m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Comp1VolumeFraction m_Compartment2Box m_Comp2VolumeFraction m_Compartment3Box m_Comp3VolumeFraction m_Compartment4Box m_Comp4VolumeFraction m_AddNoise m_NoiseDistributionBox m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddAliasing m_WrapBox m_AddDistortions m_FrequencyMapBox m_AddMotion m_RandomMotion m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml index 3820786c62..7814e573c5 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml @@ -1,83 +1,80 @@ This perspective contains all views necessary to post process fibers. - - - diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml index fbf723ec1d..668eebc1cc 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml @@ -1,29 +1,29 @@ - + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp index 70c55d4280..b3539be4a4 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp @@ -1,50 +1,51 @@ /*=================================================================== 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 "QmitkDIAppIVIMPerspective.h" #include "berryIViewLayout.h" void QmitkDIAppIVIMPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// left->AddView("org.mitk.views.ivim"); berry::IViewLayout::Pointer lo = layout->GetViewLayout("org.mitk.views.ivim"); left->AddView("org.mitk.views.segmentation"); lo = layout->GetViewLayout("org.mitk.views.segmentation"); - + left->AddView("org.mitk.views.diffusionquantification"); + left->AddView("org.mitk.views.diffusionpreprocessing"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui index 9eda318b11..455d1cef01 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui @@ -1,1172 +1,1172 @@ QmitkIVIMViewControls 0 0 - 379 + 380 1563 0 0 QmitkTemplate 9 9 9 9 Intra Voxel Incoherent Motion Estimation 0 9 0 0 Please Select Input Data Optional ROI image ROI: DWI to analyze <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> Optional ROI image <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> DWI to analyze Raw DWI: QFrame::NoFrame QFrame::Raised 0 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 warning display Qt::RichText true QFrame::StyledPanel QFrame::Raised 0 0 0 0 0 - 1 + 0 0 0 IVIM Parameters 9 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 80 16777215 D* 100 60 Qt::Horizontal 51 16777215 200 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter QFrame::NoFrame QFrame::Raised 0 0 0 0 0 80 16777215 neglect b< 250 34 Qt::Horizontal 51 16777215 46.5 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter QFrame::NoFrame QFrame::Raised 0 0 0 0 0 80 16777215 #iterations 100 10 Qt::Horizontal 30 16777215 TextLabel Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter QFrame::NoFrame QFrame::Raised 0 0 0 0 0 80 16777215 lambda 1000 10 Qt::Horizontal 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0 0 30 16777215 TextLabel Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 15 16777215 Calculate threshold from histogram * QFrame::NoFrame QFrame::Plain 0 0 0 0 0 80 16777215 neglect Si< 100 0 Qt::Horizontal 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0 0 30 16777215 TextLabel Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 15 16777215 Calculate threshold from histogram * QFrame::NoFrame QFrame::Raised 0 0 0 0 80 0 Output Images f true D false D* false true 0 0 0 400 0 0 0 0 Choose Method 2 3 Param. Fit Fit D & f with fixed D* value Fit D & f (high b), then fit D* Linearly fit D & f (high b), then fit D* Regularized Kurtosis QFrame::StyledPanel QFrame::Raised 2 2 2 2 2 Smoothing sigma Select Fit Type Omit b=0 Measurement 80 0 Output Images Force the fitting of K to remain within the given boundaries Boundaries for K Select if the data is fitted directly (straight) or the logarithmic equation is used Straight Fit Logarithmic Fit 2 QLayout::SetMaximumSize D false K true Signa for gaussian smoothing applied prior to map computation 1.000000000000000 5.000000000000000 0.100000000000000 On 0 0 0 400 Generate Output Images QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Datapoints to Clipboard Parameters to Clipboard QmitkIVIMWidget QWidget
QmitkIVIMWidget.h
1 QmitkKurtosisWidget QWidget
QmitkKurtosisWidget.h
1 ctkRangeWidget QWidget
ctkRangeWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake index 51228b5c78..aca387a866 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake @@ -1,62 +1,66 @@ set(SRC_CPP_FILES QmitkODFDetailsWidget.cpp QmitkODFRenderWidget.cpp QmitkResidualAnalysisWidget.cpp QmitkResidualViewWidget.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp + Perspectives/QmitkReconstructionPerspective.cpp + QmitkQBallReconstructionView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkODFDetailsView.cpp ) set(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkODFDetailsViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h + src/internal/Perspectives/QmitkReconstructionPerspective.h + src/internal/QmitkQBallReconstructionView.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkODFDetailsView.h src/QmitkODFRenderWidget.h src/QmitkODFDetailsWidget.h src/QmitkResidualAnalysisWidget.h src/QmitkResidualViewWidget.h ) set(CACHED_RESOURCE_FILES plugin.xml resources/quantification.png resources/OdfDetails.png resources/reconodf.png resources/recontensor.png resources/tensor.png resources/qball.png ) set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml index aa45e53c8e..de0851208f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml @@ -1,87 +1,99 @@ Q-Ball reconstruction view Calculation of tensor and Q-ball derived measures. + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp similarity index 86% copy from Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp copy to Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp index 9fee132fe5..d1c156a3ec 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp @@ -1,50 +1,52 @@ /*=================================================================== 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 "QmitkGibbsTractographyPerspective.h" +#include "QmitkReconstructionPerspective.h" #include "berryIViewLayout.h" -void QmitkGibbsTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) +void QmitkReconstructionPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// left->AddView("org.mitk.views.tensorreconstruction"); left->AddView("org.mitk.views.qballreconstruction"); - left->AddView("org.mitk.views.gibbstracking"); + left->AddView("org.mitk.views.diffusionquantification"); + left->AddView("org.mitk.views.diffusionpreprocessing"); + left->AddView("org.mitk.views.odfdetails"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h new file mode 100644 index 0000000000..f0f64719c5 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h @@ -0,0 +1,36 @@ +/*=================================================================== + +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 QmitkReconstructionPerspective_H_ +#define QmitkReconstructionPerspective_H_ + +#include + +class QmitkReconstructionPerspective : public QObject, public berry::IPerspectiveFactory +{ + Q_OBJECT + Q_INTERFACES(berry::IPerspectiveFactory) + +public: + + QmitkReconstructionPerspective() {} + ~QmitkReconstructionPerspective() {} + + void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; +}; + +#endif /* QmitkReconstructionPerspective_H_ */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp index 63e3cdc9b2..ceb16b327a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp @@ -1,44 +1,47 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include "src/internal/QmitkQBallReconstructionView.h" #include "src/internal/QmitkTensorReconstructionView.h" #include "src/internal/QmitkDiffusionQuantificationView.h" #include "src/internal/QmitkODFDetailsView.h" +#include "src/internal/Perspectives/QmitkReconstructionPerspective.h" ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { + BERRY_REGISTER_EXTENSION_CLASS(QmitkReconstructionPerspective, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox index 247f8c0607..45e9e2ca1c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -1,40 +1,38 @@ /** \page org_mitk_views_gibbstracking Global Gibbs Tractography This view provides the user interface for the global Gibbs tractography algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. \tableofcontents -\imageMacro{gibbstrackingview.png,"The Gibbs Tracking View",2} - \section QmitkGibbsTrackingUserManualInputData Input Data Mandatory Input: \li One Q-Ball or tensor image selected in the datamanager Optional Input: \li Mask Image: White matter probability mask. Corresponds to the probability to generate fiber segments in the respective voxel. \section QmitkGibbsTrackingUserManualParameters Q-Ball Reconstruction -\li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Recommended: 10^8 to 5x10^8 iterations for full brain tractography. +\li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Recommended: minimum 10^8 iterations for full brain tractography. \li Particle length/width/weight controlling the contribution of each particle to the model M \li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) \li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). \li Minimum fiber length constraint (in mm). Shorter fibers are discarded after the tracking. The automatic selection of parameters for the particle length/width and weight are determined directly from the input image using information about the image spacing and GFA. \imageMacro{gibbstrackingviewadvanced.png,"Advanced Tracking Parameters",10.08} \section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. The button next to this checkbox allows the visualization of only the next iteration step. \section QmitkGibbsTrackingUserManualReferences References [1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox index 7ddd68f71d..9e45d2e5d3 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox @@ -1,51 +1,50 @@ /** \page org_mitk_views_mlbtview Machine Learning Based Streamline Tractography This view provides the user interface for machine-learning based streamline fiber tractography on diffusion-weighted images. It is dived in two parts: (1) training of the random-forest classifier used for tractography and (2) the actual tractography. Available sections: - \ref MlbstUserManualTraining - \ref MlbstUserManualTractography - \ref MlbstUserManualReferences \section MlbstUserManualTraining Training -Before - Parameters: \li Num. Trees: Number of trees that constitute the random forest. The default of 30 works well for most cases. \li Max. Depth: Maximum tree depth. -\li Non-WM Sampling Points: Number of randomly placed sampling points in each non-white-matter voxel. These sampling points are needed to train the classifier for non-fiber tissue. \li Sample Fraction: Fraction of randomly drawn samples used to train each tree. -\li Step Size: The fibers are resampled with this step size. Influences the number of white-matter sampling ponts. Defaul is 0.5*min. voxel size. +\li Non-WM Sampling Points: Number of randomly placed sampling points in each non-white-matter voxel. These sampling points are needed to train the classifier for non-fiber tissue. +\li Fiber Sampling: The fibers are resampled equidistantly. This influences the number of white-matter sampling ponts. Defaul is 0.5*min. voxel size. \section MlbstUserManualTractography Tractography Parameters and options: \li Input DWI: Input diffusion-weighted image for tractography. Minimum number of gradient directions is 28, since 6th order spherical harmonics are used to spherically interpolate the raw signal. -\li Num. Seeds: Number of seed points per voxel. If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel. +\li Seeds per Voxel: Number of seed points per voxel. If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel. \li Step Size: The algorithm proceeds along the streamline with a fixed stepsize (in voxels). Default is 0.5*minSpacing. -\li Angular Threshold: Sudden directional changes larger than the specified angle have a probability of 0. -\li Num. Samples: Number of samples used to probe the local neighborhood. \li Sampling Distance: Maximum distance of the sampling points from the current streamline position (in voxel). +\li Num. Samples: Number of samples used to probe the local neighborhood. \li Min. Length: Shorter fibers are discarded. \li Max. Length: Longer fibers are discarded. -\li Num. Threads: Number of threads used for tractography. Default is the maximum number of threads. If demo mode is enabled, the number of threads is automatically set to 1. -\li Random sampling: If checked, the neighborhood sampling points are distributed randomly in the current neighborhood, as oposed to spherically around the current position (default). -\li Avoid premature termination: Uses the information of the neighborhood sampling points to avoid a premature fiber termination. If unchecked, no neighborhood samples are used. -\li Secondary curvature check: If checked, a secondary curvature threshold is applied and the fiber progression stops if exceeded. This can also be done a posteriory in the Fiber Processing View. -\li Mask Image: Binary image used to limit the tractography space. If no mask image is selected, the whole image volume is included in the tractography process. Typically select a binary brain mask here. -\li Seed Image: Binary image used to define the seed voxels. If no image is selected, seeds are placed in all voxels. -\li Stop Image: Binary image to define stopping regions for the tractography process. As soon as a streamline enters a region defined by this image, the streamline progression stops. Binary gray matter segmentations are a typical input here. +\li Enable Gray Matter Seeding: Seeds are onyl placed inside of the gray matter. Needs tissue label image. +\li Only Frontal Samples: Only use neighborhood samples in front of the current streamline position. +\li Mask Image: Binary mask used to constrain the generated streamlines. Streamlines can not leave the mask area. +\li Seed Image: Binary mask used to define the seed voxels. If no seed mask is specified, the whole image volume is seeded. +\li Stop Image: Binary mask used to define stopping regions. Streamlines that enter the mask area are stopped immediately. +\li Tissue Image: Tissue label image needed for gray matter seeding (WM=3, GM=1). Use e.g. MRtrix 5ttgen to generate such a label image. + \li Demo Mode: Directly visualizes the streamline progression and the sampling points. Only use this for demonstration purposes, since it is very slow. \section MlbstUserManualReferences References -[1] Neher, P.F., Götz, M., Norajitra, T., Weber, C., Maier-Hein, K.H., 2015. A machine learning based approach to fiber tractography, in: Proceedings of International Society of Magnetic Resonance in Medicine. +[1] Neher, P.F., Côte, M-A., Houde, J-C., Descoteaux, M., Maier-Hein, K.H., 2017. Fiber tractography using machine learning, doi: https://doi.org/10.1101/104190. + +[2] Neher, P.F., Götz, M., Norajitra, T., Weber, C., Maier-Hein, K.H., 2015. A machine learning based approach to fiber tractography, in: Proceedings of International Society of Magnetic Resonance in Medicine. -[2] Neher, P.F., Götz, M., Norajitra, T., Weber, C., Maier-Hein, K.H., 2015. A machine learning based approach to fiber tractography using classifier voting, in: Proceedings of Medical Image Computing and Computer-Assisted Intervention. Presented at the Medical Image Computing and Computer-Assisted Intervention. +[3] Neher, P.F., Götz, M., Norajitra, T., Weber, C., Maier-Hein, K.H., 2015. A machine learning based approach to fiber tractography using classifier voting, in: Proceedings of Medical Image Computing and Computer-Assisted Intervention. Presented at the Medical Image Computing and Computer-Assisted Intervention. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox index 546ba0a466..83ee7a336c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox @@ -1,51 +1,58 @@ /** \page org_mitk_views_streamlinetracking Streamline Tractography Available sections: - \ref StrTrackUserManualInputData + - \ref StrTrackUserManualInteractive - \ref StrTrackUserManualParameters + - \ref StrTrackUserManualAdvancedParameters - \ref StrTrackUserManualReferences \section StrTrackUserManualInputData Input Data Input: \li One or multiple DTI images selected in the datamanager. \li One ODF image (e.g. obtained using MITK Q-ball reconstruction or MRtrix CSD). \li One peak image in MRtrix format (4D float image). Optional Input: \li Binary mask used to define the seed voxels. If no seed mask is specified, the whole image volume is seeded. \li Binary mask used to constrain the generated streamlines. Streamlines can not leave the mask area. \li Binary mask used to define stopping regions. Streamlines that enter the mask area are stopped immediately. \li Tissue label image needed for gray matter seeding (WM=3, GM=1). Use e.g. MRtrix 5ttgen to generate such a label image. \li FA/GFA image used to determine streamline termination. If no image is specified, the FA/GFA image is automatically calculated from the input image. If multiple tensor images are used as input, it is recommended to provide such an image since the FA maps calculated from the individual input tensor images can not provide a suitable termination criterion. +\section StrTrackUserManualInteractive Interactive Tractography + +Interactive tractography enables the dynamic placement of spherical seed regions simply by clicking into the image. Parameters are the number of seed points and the radius of the spherical seed region. The seed points are randomly distributed inside the sphere around the selected position. By clicking and holding the left mouse button while moving the mouse around the image, the fiber connections originating from the selected region can be explored dynamically. + \section StrTrackUserManualParameters Parameters \li Mode: Toggle between deterministic and probabilistic tractography. Peak tracking only supports deterministic mode. The probabilistic method simply samples the output direction from the discrete probability ditribution provided by the discretized ODF. \li Seeds per voxel: If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel. \li Max. num. fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed. \li Cutoff: If the streamline reaches a position with an FA value or peak magnitude lower than the speciefied threshold, tracking is terminated. -\section StrTrackUserManualParameters Advanced Parameters +\section StrTrackUserManualAdvancedParameters Advanced Parameters \li Step Size: The algorithm proceeds along the streamline with a fixed stepsize. Default is 0.5*minSpacing. \li Angular threshold: Maximum angle between two successive steps (in degree). Default is 90° * step_size. For probabilistic tractography, candidate directions exceeding this threshold have probability 0, i.e. the respective ODF value is set to zero. The probabilities of the valid directions are normalized to sum to 1. \li Min. Tract Length: Shorter fibers are discarded. \li f and g values to balance between FACT [1] and TEND [2,3] tracking (only for tensor based tractography). For further information please refer to [2,3] \li Flip directions: Internally flips progression directions. This might be necessary depending on the input data. \li Neighborhood Samples: Number of neighborhood samples that are used to determine the next fiber progression direction [4]. \li Compress Fibers: Whole brain tractograms obtained with a small step size can contain billions of points. The tractograms can be compressed by removing points that do not really contribute to the fiber shape, such as many points on a straight line. An error threshold (in mm) can be defined to specify which points should be removed and which not. \li Enable Trilinear Interpolation: By default the image values are interpolated. Keep in mind that in the noninterpolated case, the TEND term is only applied once per voxel. In the interpolated case the TEND term is applied at each integration step which results in much higher curvatures and has to be compensated by an according choice of f and g. -\li Min-max normalize ODFs - +\li Min-max normalize ODFs: ODFs are min-max normalized before tractography. This results in sharper ODFs. +\li Output Probability Map: No streamline are generated. Instead, the tractography outputs a probability map that indicates the probability of a fiber to reach a voxel from the selected seed region. For this measure to be sensible, the number of seeds per voxel needs to be rather large. This option does not work during interactive tractography. +\li Enable Gray Matter Seeding: Seeds are onyl placed inside of the gray matter. Needs tissue label image. \section StrTrackUserManualReferences References [1] Mori et al. Annals Neurology 1999\n [2] Weinstein et al. Proceedings of IEEE Visualization 1999\n [3] Lazar et al. Human Brain Mapping 2003\n */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml index cb8e17d18f..8d5bc44888 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml @@ -1,115 +1,108 @@ - - + --> + + + - - - - - - - - - - diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp index 9fee132fe5..7c043d6050 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp @@ -1,50 +1,50 @@ /*=================================================================== 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 "QmitkGibbsTractographyPerspective.h" #include "berryIViewLayout.h" void QmitkGibbsTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// - left->AddView("org.mitk.views.tensorreconstruction"); - left->AddView("org.mitk.views.qballreconstruction"); left->AddView("org.mitk.views.gibbstracking"); + left->AddView("org.mitk.views.qballreconstruction"); + left->AddView("org.mitk.views.tensorreconstruction"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkMachineLearningTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkMachineLearningTractographyPerspective.cpp index 74e31c3612..dee7fc5715 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkMachineLearningTractographyPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkMachineLearningTractographyPerspective.cpp @@ -1,50 +1,50 @@ /*=================================================================== 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 "QmitkMachineLearningTractographyPerspective.h" #include "berryIViewLayout.h" void QmitkMachineLearningTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// - left->AddView("org.mitk.views.diffusionpreprocessing"); - left->AddView("org.mitk.views.segmentation"); left->AddView("org.mitk.views.mlbtview"); + left->AddView("org.mitk.views.segmentation"); + left->AddView("org.mitk.views.diffusionpreprocessing"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp index 03b705d96e..3cc35a996e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp @@ -1,50 +1,49 @@ /*=================================================================== 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 "QmitkStreamlineTractographyPerspective.h" #include "berryIViewLayout.h" void QmitkStreamlineTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// - left->AddView("org.mitk.views.tensorreconstruction"); - left->AddView("org.mitk.views.segmentation"); left->AddView("org.mitk.views.streamlinetracking"); + left->AddView("org.mitk.views.segmentation"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTView.cpp index 523379b757..266c9c254c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTView.cpp @@ -1,449 +1,452 @@ /*=================================================================== 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 // Qmitk #include "QmitkMLBTView.h" // Qt #include #include #include #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkMLBTView::VIEW_ID = "org.mitk.views.mlbtview"; using namespace berry; QmitkMLBTView::QmitkMLBTView() : QmitkAbstractView() , m_Controls( 0 ) { m_TrackingTimer = std::make_shared(this); m_LastLoadedForestName = "(none)"; m_ForestHandler = new mitk::TrackingHandlerRandomForest<6,100>(); } // Destructor QmitkMLBTView::~QmitkMLBTView() { delete m_ForestHandler; } void QmitkMLBTView::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::QmitkMLBTViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_StartTrainingButton, SIGNAL ( clicked() ), this, SLOT( StartTrainingThread() ) ); connect( &m_TrainingWatcher, SIGNAL ( finished() ), this, SLOT( OnTrainingThreadStop() ) ); connect( m_Controls->m_StartTrackingButton, SIGNAL ( clicked() ), this, SLOT( StartTrackingThread() ) ); connect( &m_TrackingWatcher, SIGNAL ( finished() ), this, SLOT( OnTrackingThreadStop() ) ); connect( m_Controls->m_SaveForestButton, SIGNAL ( clicked() ), this, SLOT( SaveForest() ) ); connect( m_Controls->m_LoadForestButton, SIGNAL ( clicked() ), this, SLOT( LoadForest() ) ); connect( m_TrackingTimer.get(), SIGNAL(timeout()), this, SLOT(BuildFibers()) ); connect( m_Controls->m_TimerIntervalBox, SIGNAL(valueChanged(int)), this, SLOT( ChangeTimerInterval(int) )); connect( m_Controls->m_DemoModeBox, SIGNAL(stateChanged(int)), this, SLOT( ToggleDemoMode(int) )); connect( m_Controls->m_PauseTrackingButton, SIGNAL ( clicked() ), this, SLOT( PauseTracking() ) ); connect( m_Controls->m_AbortTrackingButton, SIGNAL ( clicked() ), this, SLOT( AbortTracking() ) ); connect( m_Controls->m_AddTwButton, SIGNAL ( clicked() ), this, SLOT( AddTrainingWidget() ) ); connect( m_Controls->m_RemoveTwButton, SIGNAL ( clicked() ), this, SLOT( RemoveTrainingWidget() ) ); m_Controls->m_TrackingMaskImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TrackingSeedImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TrackingStopImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TrackingRawImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TissueImageBox->SetDataStorage(this->GetDataStorage()); mitk::NodePredicateIsDWI::Pointer isDiffusionImage = mitk::NodePredicateIsDWI::New(); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_TissueImageBox->SetPredicate(finalPredicate); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); finalPredicate = mitk::NodePredicateAnd::New(finalPredicate, isBinaryPredicate); m_Controls->m_TrackingMaskImageBox->SetPredicate(finalPredicate); m_Controls->m_TrackingSeedImageBox->SetPredicate(finalPredicate); m_Controls->m_TrackingStopImageBox->SetPredicate(finalPredicate); m_Controls->m_TrackingRawImageBox->SetPredicate(isDiffusionImage); m_Controls->m_TrackingMaskImageBox->SetZeroEntryText("--"); m_Controls->m_TrackingSeedImageBox->SetZeroEntryText("--"); m_Controls->m_TrackingStopImageBox->SetZeroEntryText("--"); m_Controls->m_TissueImageBox->SetZeroEntryText("--"); AddTrainingWidget(); UpdateGui(); } } void QmitkMLBTView::AddTrainingWidget() { std::shared_ptr tw = std::make_shared(); tw->SetDataStorage(this->GetDataStorage()); m_Controls->m_TwFrame->layout()->addWidget(tw.get()); m_TrainingWidgets.push_back(tw); } void QmitkMLBTView::RemoveTrainingWidget() { if(m_TrainingWidgets.size()>1) { m_TrainingWidgets.back().reset(); m_TrainingWidgets.pop_back(); } } void QmitkMLBTView::UpdateGui() { if (m_ForestHandler->IsForestValid()) { std::string label_text="Random forest available: "+m_LastLoadedForestName; m_Controls->statusLabel->setText( QString(label_text.c_str()) ); m_Controls->m_SaveForestButton->setEnabled(true); m_Controls->m_StartTrackingButton->setEnabled(true); } else { m_Controls->statusLabel->setText("Please load or train random forest!"); m_Controls->m_SaveForestButton->setEnabled(false); m_Controls->m_StartTrackingButton->setEnabled(false); } } void QmitkMLBTView::SetFocus() { m_Controls->toolBox->setFocus(); } void QmitkMLBTView::AbortTracking() { if (tracker.IsNotNull()) { tracker->m_AbortTracking = true; } } void QmitkMLBTView::PauseTracking() { if (tracker.IsNotNull()) { tracker->m_PauseTracking = !tracker->m_PauseTracking; } } void QmitkMLBTView::ChangeTimerInterval(int value) { m_TrackingTimer->setInterval(value); } void QmitkMLBTView::ToggleDemoMode(int state) { if (tracker.IsNotNull()) { tracker->SetDemoMode(m_Controls->m_DemoModeBox->isChecked()); tracker->m_Stop = false; } } void QmitkMLBTView::BuildFibers() { if (m_Controls->m_DemoModeBox->isChecked() && tracker.IsNotNull() && tracker->m_BuildFibersFinished) { vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); outFib->SetFiberColors(255,255,255); m_TractogramNode->SetData(outFib); m_SamplingPointsNode->SetData(tracker->m_SamplingPointset); m_AlternativePointsNode->SetData(tracker->m_AlternativePointset); m_StopVotePointsNode->SetData(tracker->m_StopVotePointset); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); tracker->m_BuildFibersFinished = false; tracker->m_BuildFibersReady = 0; tracker->m_Stop = false; } } void QmitkMLBTView::LoadForest() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Forest"), QDir::currentPath(), tr("HDF5 random forest file (*.rf)") ); if(filename.isEmpty() || filename.isNull()) return; m_ForestHandler->LoadForest( filename.toStdString() ); QFileInfo fi( filename ); m_LastLoadedForestName = QString( fi.baseName() + "." + fi.completeSuffix() ).toStdString(); UpdateGui(); } void QmitkMLBTView::StartTrackingThread() { m_TractogramNode = mitk::DataNode::New(); m_TractogramNode->SetName("MLBT Result"); //m_TractogramNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(20)); m_TractogramNode->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(true)); m_TractogramNode->SetProperty("LineWidth", mitk::IntProperty::New(1)); //m_TractogramNode->SetProperty("color",mitk::ColorProperty::New(0, 1, 1)); this->GetDataStorage()->Add(m_TractogramNode); m_SamplingPointsNode = mitk::DataNode::New(); m_SamplingPointsNode->SetName("SamplingPoints"); m_SamplingPointsNode->SetProperty("pointsize", mitk::FloatProperty::New(0.2)); m_SamplingPointsNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); mitk::PointSetShapeProperty::Pointer bla = mitk::PointSetShapeProperty::New(); bla->SetValue(8); m_SamplingPointsNode->SetProperty("Pointset.2D.shape", bla); m_SamplingPointsNode->SetProperty("Pointset.2D.distance to plane", mitk::FloatProperty::New(1.5)); m_SamplingPointsNode->SetProperty("point 2D size", mitk::FloatProperty::New(0.1)); m_SamplingPointsNode->SetProperty("Pointset.2D.fill shape", mitk::BoolProperty::New(true)); this->GetDataStorage()->Add(m_SamplingPointsNode); m_AlternativePointsNode = mitk::DataNode::New(); m_AlternativePointsNode->SetName("AlternativePoints"); m_AlternativePointsNode->SetProperty("pointsize", mitk::FloatProperty::New(0.2)); m_AlternativePointsNode->SetProperty("color", mitk::ColorProperty::New(0,1,0)); m_AlternativePointsNode->SetProperty("Pointset.2D.shape", bla); m_AlternativePointsNode->SetProperty("Pointset.2D.distance to plane", mitk::FloatProperty::New(1.5)); m_AlternativePointsNode->SetProperty("point 2D size", mitk::FloatProperty::New(0.1)); m_AlternativePointsNode->SetProperty("Pointset.2D.fill shape", mitk::BoolProperty::New(true)); this->GetDataStorage()->Add(m_AlternativePointsNode); m_StopVotePointsNode = mitk::DataNode::New(); m_StopVotePointsNode->SetName("StopVotes"); m_StopVotePointsNode->SetProperty("pointsize", mitk::FloatProperty::New(0.2)); m_StopVotePointsNode->SetProperty("color", mitk::ColorProperty::New(1,0,0)); m_StopVotePointsNode->SetProperty("Pointset.2D.shape", bla); m_StopVotePointsNode->SetProperty("Pointset.2D.distance to plane", mitk::FloatProperty::New(1.5)); m_StopVotePointsNode->SetProperty("point 2D size", mitk::FloatProperty::New(0.1)); m_StopVotePointsNode->SetProperty("Pointset.2D.fill shape", mitk::BoolProperty::New(true)); this->GetDataStorage()->Add(m_StopVotePointsNode); QFuture future = QtConcurrent::run( this, &QmitkMLBTView::StartTracking ); m_TrackingWatcher.setFuture(future); m_TrackingThreadIsRunning = true; m_Controls->m_StartTrackingButton->setEnabled(false); m_TrackingTimer->start(m_Controls->m_TimerIntervalBox->value()); } void QmitkMLBTView::OnTrackingThreadStop() { m_TrackingThreadIsRunning = false; m_Controls->m_StartTrackingButton->setEnabled(true); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); m_TractogramNode->SetData(outFib); m_TractogramNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(1)); if (m_Controls->m_DemoModeBox->isChecked()) { m_SamplingPointsNode->SetData(tracker->m_SamplingPointset); m_AlternativePointsNode->SetData(tracker->m_AlternativePointset); } tracker = nullptr; m_TrackingTimer->stop(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkMLBTView::StartTracking() { if ( m_Controls->m_TrackingRawImageBox->GetSelectedNode().IsNull() || !m_ForestHandler->IsForestValid()) return; mitk::Image::Pointer dwi = dynamic_cast(m_Controls->m_TrackingRawImageBox->GetSelectedNode()->GetData()); m_ForestHandler->AddDwi(dwi); m_ForestHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); // int numThread = itk::MultiThreader::GetGlobalDefaultNumberOfThreads(); tracker = TrackerType::New(); tracker->SetDemoMode(m_Controls->m_DemoModeBox->isChecked()); if (m_Controls->m_DemoModeBox->isChecked()) tracker->SetNumberOfThreads(1); if (m_Controls->m_TrackingMaskImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mask = dynamic_cast(m_Controls->m_TrackingMaskImageBox->GetSelectedNode()->GetData()); ItkUcharImgType::Pointer itkMask = ItkUcharImgType::New(); mitk::CastToItkImage(mask, itkMask); tracker->SetMaskImage(itkMask); } if (m_Controls->m_TrackingSeedImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TrackingSeedImageBox->GetSelectedNode()->GetData()); ItkUcharImgType::Pointer itkImg = ItkUcharImgType::New(); mitk::CastToItkImage(img, itkImg); tracker->SetSeedImage(itkImg); } if (m_Controls->m_TrackingStopImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TrackingStopImageBox->GetSelectedNode()->GetData()); ItkUcharImgType::Pointer itkImg = ItkUcharImgType::New(); mitk::CastToItkImage(img, itkImg); tracker->SetStoppingRegions(itkImg); } if (m_Controls->m_TissueImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TissueImageBox->GetSelectedNode()->GetData()); ItkUcharImgType::Pointer itkImg = ItkUcharImgType::New(); mitk::CastToItkImage(img, itkImg); tracker->SetTissueImage(itkImg); } tracker->SetSeedsPerVoxel(m_Controls->m_NumberOfSeedsBox->value()); tracker->SetStepSize(m_Controls->m_TrackingStepSizeBox->value()); tracker->SetMinTractLength(m_Controls->m_MinLengthBox->value()); tracker->SetMaxTractLength(m_Controls->m_MaxLengthBox->value()); - tracker->SetAposterioriCurvCheck(m_Controls->m_Curvcheck2->isChecked()); + tracker->SetAposterioriCurvCheck(false); tracker->SetNumberOfSamples(m_Controls->m_NumSamplesBox->value()); - tracker->SetAvoidStop(m_Controls->m_AvoidStop->isChecked()); tracker->SetTrackingHandler(m_ForestHandler); tracker->SetSamplingDistance(m_Controls->m_SamplingDistanceBox->value()); - tracker->SetDeflectionMod(m_Controls->m_DeflectionModBox->value()); - tracker->SetRandomSampling(m_Controls->m_RandomSampling->isChecked()); - tracker->SetUseStopVotes(m_Controls->m_UseStopVotes->isChecked()); + tracker->SetUseStopVotes(m_Controls->m_OnlyForwardSamples->isChecked()); tracker->SetOnlyForwardSamples(m_Controls->m_OnlyForwardSamples->isChecked()); tracker->SetNumPreviousDirections(m_Controls->m_NumPrevDirs->value()); tracker->SetSeedOnlyGm(m_Controls->m_SeedGm->isChecked()); - tracker->SetAngularThreshold(45); tracker->Update(); } void QmitkMLBTView::SaveForest() { if (!m_ForestHandler->IsForestValid()) { UpdateGui(); return; } QString filename = QFileDialog::getSaveFileName(0, tr("Save Forest"), QDir::currentPath()+"/forest.rf", tr("HDF5 random forest file (*.rf)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".rf")) filename += ".rf"; m_ForestHandler->SaveForest( filename.toStdString() ); } void QmitkMLBTView::StartTrainingThread() { if (!this->IsTrainingInputValid()) { QMessageBox::warning(nullptr, "Training aborted", "Training could not be started. Not all necessary datasets were selected."); return; } QFuture future = QtConcurrent::run( this, &QmitkMLBTView::StartTraining ); m_TrainingWatcher.setFuture(future); m_Controls->m_StartTrainingButton->setEnabled(false); + m_Controls->m_StartTrainingButton->setText("Training in progress ..."); + m_Controls->m_StartTrainingButton->setToolTip("Training in progress. This can take up to a couple of hours."); + m_Controls->m_StartTrainingButton->setCursor(Qt::WaitCursor); + QApplication::processEvents(); m_Controls->m_SaveForestButton->setEnabled(false); m_Controls->m_LoadForestButton->setEnabled(false); } void QmitkMLBTView::OnTrainingThreadStop() { m_Controls->m_StartTrainingButton->setEnabled(true); m_Controls->m_SaveForestButton->setEnabled(true); m_Controls->m_LoadForestButton->setEnabled(true); + m_Controls->m_StartTrainingButton->setCursor(Qt::ArrowCursor); + m_Controls->m_StartTrainingButton->setText("Start Training"); + m_Controls->m_StartTrainingButton->setToolTip("Start Training. This can take up to a couple of hours."); + m_LastLoadedForestName = "new_forest"; UpdateGui(); + QApplication::processEvents(); } void QmitkMLBTView::StartTraining() { std::vector< mitk::Image::Pointer > m_SelectedDiffImages; std::vector< mitk::FiberBundle::Pointer > m_SelectedFB; std::vector< ItkUcharImgType::Pointer > m_MaskImages; std::vector< ItkUcharImgType::Pointer > m_WhiteMatterImages; for (auto w : m_TrainingWidgets) { m_SelectedDiffImages.push_back(dynamic_cast(w->GetImage()->GetData())); m_SelectedFB.push_back(dynamic_cast(w->GetFibers()->GetData())); if (w->GetMask().IsNotNull()) { mitk::Image::Pointer img = dynamic_cast(w->GetMask()->GetData()); ItkUcharImgType::Pointer itkMask = ItkUcharImgType::New(); mitk::CastToItkImage(img, itkMask); m_MaskImages.push_back(itkMask); } else m_MaskImages.push_back(nullptr); if (w->GetWhiteMatter().IsNotNull()) { mitk::Image::Pointer img = dynamic_cast(w->GetWhiteMatter()->GetData()); ItkUcharImgType::Pointer itkMask = ItkUcharImgType::New(); mitk::CastToItkImage(img, itkMask); m_WhiteMatterImages.push_back(itkMask); } else m_WhiteMatterImages.push_back(nullptr); } m_ForestHandler->SetDwis(m_SelectedDiffImages); m_ForestHandler->SetTractograms(m_SelectedFB); m_ForestHandler->SetMaskImages(m_MaskImages); m_ForestHandler->SetWhiteMatterImages(m_WhiteMatterImages); m_ForestHandler->SetNumTrees(m_Controls->m_NumTreesBox->value()); m_ForestHandler->SetMaxTreeDepth(m_Controls->m_MaxDepthBox->value()); m_ForestHandler->SetGrayMatterSamplesPerVoxel(m_Controls->m_GmSamplingBox->value()); m_ForestHandler->SetSampleFraction(m_Controls->m_SampleFractionBox->value()); m_ForestHandler->SetStepSize(m_Controls->m_TrainingStepSizeBox->value()); m_ForestHandler->SetNumPreviousDirections(m_Controls->m_NumPrevDirs->value()); - m_ForestHandler->SetBidirectionalFiberSampling(m_Controls->m_BidirectionalSampling->isChecked()); - m_ForestHandler->SetZeroDirWmFeatures(m_Controls->m_ZeroDirBox->isChecked()); m_ForestHandler->StartTraining(); } bool QmitkMLBTView::IsTrainingInputValid(void) const { for (auto widget : m_TrainingWidgets) { if (widget->GetImage().IsNull() || widget->GetFibers().IsNull()) { return false; } } return true; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTViewControls.ui index 86a7d00841..b1425836d6 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkMLBTViewControls.ui @@ -1,905 +1,877 @@ QmitkMLBTViewControls 0 0 503 672 Form - + + + + Please load or train random forest! + + + Qt::AlignCenter + + + + 1 0 0 485 517 Training - + + + + Qt::Vertical + + + + 20 + 40 + + + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 - - + + - Add additional training data pair + Remove training data pair ... - :/org_mitk_icons/icons/tango/scalable/actions/list-add.svg:/org_mitk_icons/icons/tango/scalable/actions/list-add.svg + :/org_mitk_icons/icons/tango/scalable/actions/list-remove.svg:/org_mitk_icons/icons/tango/scalable/actions/list-remove.svg - - + + - Remove training data pair + Add additional training data pair ... - :/org_mitk_icons/icons/tango/scalable/actions/list-remove.svg:/org_mitk_icons/icons/tango/scalable/actions/list-remove.svg + :/org_mitk_icons/icons/tango/scalable/actions/list-add.svg:/org_mitk_icons/icons/tango/scalable/actions/list-add.svg - - - - QFrame::NoFrame + + + + Start Training. This can take up to a couple of hours. - - QFrame::Raised + + Start Training - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - 6 - - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Input DWI: - - - Qt::AlignCenter - - - - - - - Reference Tractogram: - - - Qt::AlignCenter - - - - - - - Mask: - - - Qt::AlignCenter - - - - - - - WM: - - - Qt::AlignCenter - - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - + + - Start Training + Save Forest - - - - Use direction as well as zero-vector as directional training feature at each point. This enables to learn to predict the direction without a previous direction (e.g. at seed point). - + + - Zero-direction features + <html><head/><body><p><span style=" font-weight:600; color:#ff0000;">It is recommended to use the command line application 'RfTraining' instead of this graphical user interface for the training process.</span></p><p><span style=" font-weight:600; color:#ff0000;">The GUI is intended for testing using smaller examples.</span></p></body></html> - + + Qt::RichText + + + Qt::AlignCenter + + true + + 5 + - + QFrame::NoFrame QFrame::Raised 0 0 0 0 - - - - Maximum tree depth. + + + + Number of tress in the final random forest. 1 999999999 - 25 - - - - - - - Non-WM Sampling Points: + 30 - + Fiber Sampling: - - - - Number of tress in the final random forest. + + + + Maximum tree depth. 1 999999999 - 30 + 25 - + + + + Fraction of samples used to train each tree. + + + 3 + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.700000000000000 + + + + Fiber sampling in mm. Determines the number of white-matter samples (-1 = auto). 3 -1.000000000000000 999.000000000000000 0.100000000000000 -1.000000000000000 + + + + Non-WM Sampling Points: + + + Num. Trees: - + + + + Max. Depth: + + + + Number of sampling points outside of the white-matter (-1 = automatic estimation). -1 999999999 -1 - - - - Max. Depth: - - - - + Sample Fraction: - - - - Fraction of samples used to train each tree. - - - 3 - - - 1.000000000000000 - - - 0.100000000000000 - - - 0.700000000000000 - - - - - - - Save Forest - - - - - - - Sample fibers in both directions. - - - Bidirectional sampling + + + + QFrame::NoFrame - - true + + QFrame::Raised + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + 6 + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Input DWI: + + + Qt::AlignCenter + + + + + + + Reference Tractogram: + + + Qt::AlignCenter + + + + + + + Mask: + + + Qt::AlignCenter + + + + + + + WM: + + + Qt::AlignCenter + + + + + + + 0 0 471 - 657 + 524 Tractography - + + + This requires a tissue segmentation image. + - Random sampling + Enable Gray Matter Seeding false - - + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - - - - - - - 999999999.000000000000000 - - - 1.000000000000000 - - - 400.000000000000000 - - - - - - - Deflection distance modifier: - - - - - - - Number of seeds per voxel. - - - 1 - - - 999 - - - - - - - 1.000000000000000 - - - 0.100000000000000 - - - 1.000000000000000 - - - - - - - Num. Seeds: - - - - - - 0.100000000000000 - - - 0.500000000000000 - - + - - - Step Size: - - - - - + - Num. Samples: - - - - - - - 0.000000000000000 - - - - - - - 999999999.000000000000000 - - - 1.000000000000000 - - - 20.000000000000000 + Mask Image: - + - Sampling Distance: + Seed Image: - - - - Input DWI: - - + + - + - Max. Length + Stop Image: + + + - + - Min. Length + Tissue Image: - - - - Number of seeds per voxel. - - - 0 - - - 256 - - - 30 - - + + - - + + + + Only neighborhood samples in front of the current streamline position are considered. + - Secondary curvature check + Only Frontal Samples - false + true Load Forest - + + + + Qt::Vertical + + + + 20 + 40 + + + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 + + Tractigraphy is visualized in slow-motion. Single threaded. + Demo Mode 1 1000 10 - + QFrame::NoFrame QFrame::Raised 0 0 0 0 Pause tractography ... :/org_mitk_icons/icons/tango/scalable/actions/media-playback-pause.svg:/org_mitk_icons/icons/tango/scalable/actions/media-playback-pause.svg Start tractography ... :/org_mitk_icons/icons/tango/scalable/actions/media-playback-start.svg:/org_mitk_icons/icons/tango/scalable/actions/media-playback-start.svg Abort tractography ... :/org_mitk_icons/icons/tango/scalable/actions/media-playback-stop.svg:/org_mitk_icons/icons/tango/scalable/actions/media-playback-stop.svg - - - - Qt::Vertical - - - - 20 - 40 - - - - - - + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - + + + Number of neighborhood samples + + + + + + 0 + + + 256 + + + 30 + + - - + + + + Number of seeds per voxel. + + + + + + 1 + + + 999 + + + + + - Mask Image: + Seeds per Voxel: - - + + + + Maximum fiber length (in mm) + + + + + + 999999999.000000000000000 + + + 1.000000000000000 + + + 400.000000000000000 + + + + + + + + - Seed Image: + Input DWI: - - + + + + Max. Length + + - - + + - Stop Image: + Step Size: - - + + + + Minimum fiber length (in mm) + + + + + + 999999999.000000000000000 + + + 1.000000000000000 + + + 20.000000000000000 + + - - + + - Tissue Image: + Sampling Distance: - - + + + + Min. Length + + + + + + + Sampling distance (in voxels) + + + 0.100000000000000 + + + 0.250000000000000 + + + + + + + Step size (in voxels) + + + 0.500000000000000 + + + + + + + Num. Samples: + + - - - - Use stop votes - - - true - - - - - - - Avoid premature termination - - - true - - - - - - - Only frontal samples - - - true - - - - - - - Seed only GM - - - false - - - - - - - Please load or train random forest! - - - Qt::AlignCenter - - - - + Training and tractography 0 0 0 0 Num. previous directions: + + Number of previous fiber directions used as features. + - Number of seeds per voxel. + 0 50 1 - + Qt::Horizontal - QmitkDataStorageComboBox + QmitkDataStorageComboBoxWithSelectNone QComboBox -
QmitkDataStorageComboBox.h
+
QmitkDataStorageComboBoxWithSelectNone.h
 - QmitkDataStorageComboBoxWithSelectNone + QmitkDataStorageComboBox QComboBox -
QmitkDataStorageComboBoxWithSelectNone.h
+
QmitkDataStorageComboBox.h
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp index 1ba7a4f1f3..9b54bdbd44 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp @@ -1,557 +1,562 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include // VTK #include #include #include #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() : m_Controls(nullptr) { } // 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 ); m_Controls->m_FaImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_SeedImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_StopImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TissueImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate ); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate ); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); m_Controls->m_FaImageBox->SetPredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); m_Controls->m_FaImageBox->SetZeroEntryText("--"); m_Controls->m_SeedImageBox->SetPredicate( mitk::NodePredicateAnd::New(isBinaryPredicate, dimensionPredicate) ); m_Controls->m_SeedImageBox->SetZeroEntryText("--"); m_Controls->m_MaskImageBox->SetPredicate( mitk::NodePredicateAnd::New(isBinaryPredicate, dimensionPredicate) ); m_Controls->m_MaskImageBox->SetZeroEntryText("--"); m_Controls->m_StopImageBox->SetPredicate( mitk::NodePredicateAnd::New(isBinaryPredicate, dimensionPredicate) ); m_Controls->m_StopImageBox->SetZeroEntryText("--"); m_Controls->m_TissueImageBox->SetPredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); m_Controls->m_TissueImageBox->SetZeroEntryText("--"); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_InteractiveBox, SIGNAL(stateChanged(int)), this, SLOT(ToggleInteractive()) ); connect( m_Controls->m_TissueImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); m_FirstTensorProbRun = true; } UpdateGui(); } void QmitkStreamlineTrackingView::ToggleInteractive() { UpdateGui(); mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart(); if ( m_Controls->m_InteractiveBox->isChecked() ) { + QApplication::setOverrideCursor(Qt::PointingHandCursor); + QApplication::processEvents(); + m_InteractiveNode = mitk::DataNode::New(); QString name("InteractiveFib"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); m_InteractivePointSetNode = mitk::DataNode::New(); m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); m_InteractivePointSetNode->SetName("InteractiveSeedRegion"); mitk::PointSetShapeProperty::Pointer shape_prop = mitk::PointSetShapeProperty::New(); shape_prop->SetValue(mitk::PointSetShapeProperty::PointSetShape::CIRCLE); m_InteractivePointSetNode->SetProperty("Pointset.2D.shape", shape_prop); GetDataStorage()->Add(m_InteractivePointSetNode); if (renderWindow) { { mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString("axial"))->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkStreamlineTrackingView::OnSliceChanged ); m_SliceObserverTag1 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), command ); } { mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString("sagittal"))->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkStreamlineTrackingView::OnSliceChanged ); m_SliceObserverTag2 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), command ); } { mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString("coronal"))->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkStreamlineTrackingView::OnSliceChanged ); m_SliceObserverTag3 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), command ); } } } else { + QApplication::restoreOverrideCursor(); + QApplication::processEvents(); + m_InteractiveNode = nullptr; m_InteractivePointSetNode = nullptr; mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString("axial"))->GetSliceNavigationController(); slicer->RemoveObserver(m_SliceObserverTag1); slicer = renderWindow->GetQmitkRenderWindow(QString("sagittal"))->GetSliceNavigationController(); slicer->RemoveObserver(m_SliceObserverTag2); slicer = renderWindow->GetQmitkRenderWindow(QString("coronal"))->GetSliceNavigationController(); slicer->RemoveObserver(m_SliceObserverTag3); } } void QmitkStreamlineTrackingView::OnSliceChanged(const itk::EventObject& /*e*/) { std::srand(std::time(0)); m_SeedPoints.clear(); itk::Point world_pos = this->GetRenderWindowPart()->GetSelectedPosition(); m_SeedPoints.push_back(world_pos); float radius = m_Controls->m_SeedRadiusBox->value(); int num = m_Controls->m_NumSeedsBox->value(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); pointset->InsertPoint(0, world_pos); m_InteractivePointSetNode->SetProperty("pointsize", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetProperty("point 2D size", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetData(pointset); for (int i=1; i p; p[0] = rand()%1000-500; p[1] = rand()%1000-500; p[2] = rand()%1000-500; p.Normalize(); p *= radius; m_SeedPoints.push_back(world_pos+p); } DoFiberTracking(); } void QmitkStreamlineTrackingView::SetFocus() { } void QmitkStreamlineTrackingView::OnSelectionChanged( berry::IWorkbenchPart::Pointer part, const QList& nodes ) { m_InputImageNodes.clear(); m_InputImages.clear(); for( auto node : nodes ) { if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) ) { m_InputImageNodes.push_back(node); m_InputImages.push_back(dynamic_cast(node->GetData())); } else if ( dynamic_cast(node->GetData()) ) { m_InputImageNodes.push_back(node); m_InputImages.push_back(dynamic_cast(node->GetData())); } else { mitk::Image* img = dynamic_cast(node->GetData()); if (img!=nullptr) { int dim = img->GetDimension(); unsigned int* dimensions = img->GetDimensions(); if (dim==4 && dimensions[3]%3==0) { m_InputImageNodes.push_back(node); m_InputImages.push_back(dynamic_cast(node->GetData())); } } } } } UpdateGui(); } void QmitkStreamlineTrackingView::UpdateGui() { m_Controls->m_TensorImageLabel->setText("mandatory"); m_Controls->m_fBox->setVisible(false); m_Controls->m_fLabel->setVisible(false); m_Controls->m_gBox->setVisible(false); m_Controls->m_gLabel->setVisible(false); m_Controls->m_FaImageBox->setVisible(false); m_Controls->mFaImageLabel->setVisible(false); m_Controls->m_NormalizeODFsBox->setVisible(false); if (m_Controls->m_TissueImageBox->GetSelectedNode().IsNotNull()) m_Controls->m_SeedGmBox->setVisible(true); else m_Controls->m_SeedGmBox->setVisible(false); if(!m_InputImageNodes.empty()) { if (m_InputImageNodes.size()>1) m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.size()+" images selected"); else m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.at(0)->GetName().c_str()); m_Controls->m_InputData->setTitle("Input Data"); m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_InteractiveBox->setEnabled(true); if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { m_Controls->m_fBox->setVisible(true); m_Controls->m_fLabel->setVisible(true); m_Controls->m_gBox->setVisible(true); m_Controls->m_gLabel->setVisible(true); m_Controls->mFaImageLabel->setVisible(true); m_Controls->m_FaImageBox->setVisible(true); if (m_Controls->m_ModeBox->currentIndex()==1) m_Controls->m_NormalizeODFsBox->setVisible(true); } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { m_Controls->mFaImageLabel->setVisible(true); m_Controls->m_FaImageBox->setVisible(true); m_Controls->m_NormalizeODFsBox->setVisible(true); } else { } } else { m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_InteractiveBox->setEnabled(false); } } void QmitkStreamlineTrackingView::DoFiberTracking() { if (m_InputImages.empty()) return; mitk::TrackingDataHandler* trackingHandler; if( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { typedef itk::Image< itk::DiffusionTensor3D, 3> TensorImageType; typedef mitk::ImageToItk CasterType; if (m_Controls->m_ModeBox->currentIndex()==1) { if (m_InputImages.size()>1) { QMessageBox::information(nullptr, "Information", "Probabilistic tensor tractography is only implemented for single-tensor mode!"); return; } if (m_FirstTensorProbRun) { QMessageBox::information(nullptr, "Information", "Internally calculating ODF from tensor image and performing probabilistic ODF tractography. Please keep the state of the ODF normalization box (see advanced parameters) in mind. TEND parameters are ignored."); m_FirstTensorProbRun = false; } TensorImageType::Pointer itkImg = TensorImageType::New(); mitk::CastToItkImage(m_InputImages.at(0), itkImg); typedef itk::TensorImageToQBallImageFilter< float, float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkImg ); filter->Update(); typedef mitk::ImageToItk< mitk::TrackingHandlerOdf::ItkOdfImageType > CasterType; trackingHandler = new mitk::TrackingHandlerOdf(); dynamic_cast(trackingHandler)->SetOdfImage(filter->GetOutput()); dynamic_cast(trackingHandler)->SetGfaThreshold(m_Controls->m_ScalarThresholdBox->value()); dynamic_cast(trackingHandler)->SetMinMaxNormalize(m_Controls->m_NormalizeODFsBox->isChecked()); dynamic_cast(trackingHandler)->SetOdfPower(1); if (m_Controls->m_FaImageBox->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageBox->GetSelectedNode()->GetData()), itkImg); dynamic_cast(trackingHandler)->SetGfaImage(itkImg); } } else { trackingHandler = new mitk::TrackingHandlerTensor(); for (int i=0; i<(int)m_InputImages.size(); i++) { TensorImageType::Pointer itkImg = TensorImageType::New(); mitk::CastToItkImage(m_InputImages.at(i), itkImg); dynamic_cast(trackingHandler)->AddTensorImage(itkImg); } if (m_Controls->m_FaImageBox->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageBox->GetSelectedNode()->GetData()), itkImg); dynamic_cast(trackingHandler)->SetFaImage(itkImg); } dynamic_cast(trackingHandler)->SetFaThreshold(m_Controls->m_ScalarThresholdBox->value()); dynamic_cast(trackingHandler)->SetF((float)m_Controls->m_fBox->value()); dynamic_cast(trackingHandler)->SetG((float)m_Controls->m_gBox->value()); } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { typedef mitk::ImageToItk< mitk::TrackingHandlerOdf::ItkOdfImageType > CasterType; trackingHandler = new mitk::TrackingHandlerOdf(); mitk::TrackingHandlerOdf::ItkOdfImageType::Pointer itkImg = mitk::TrackingHandlerOdf::ItkOdfImageType::New(); mitk::CastToItkImage(m_InputImages.at(0), itkImg); dynamic_cast(trackingHandler)->SetOdfImage(itkImg); dynamic_cast(trackingHandler)->SetGfaThreshold(m_Controls->m_ScalarThresholdBox->value()); dynamic_cast(trackingHandler)->SetMinMaxNormalize(m_Controls->m_NormalizeODFsBox->isChecked()); if (m_Controls->m_FaImageBox->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageBox->GetSelectedNode()->GetData()), itkImg); dynamic_cast(trackingHandler)->SetGfaImage(itkImg); } } else { if (m_Controls->m_ModeBox->currentIndex()==1) { QMessageBox::information(nullptr, "Information", "Probabilstic tractography is only implementedfor ODF images."); return; } try { typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(m_InputImages.at(0)); caster->Update(); mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput(); trackingHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(trackingHandler)->SetPeakImage(itkImg); dynamic_cast(trackingHandler)->SetPeakThreshold(m_Controls->m_ScalarThresholdBox->value()); } catch(...) { return; } } trackingHandler->SetFlipX(m_Controls->m_FlipXBox->isChecked()); trackingHandler->SetFlipY(m_Controls->m_FlipYBox->isChecked()); trackingHandler->SetFlipZ(m_Controls->m_FlipZBox->isChecked()); trackingHandler->SetInterpolate(m_Controls->m_InterpolationBox->isChecked()); switch (m_Controls->m_ModeBox->currentIndex()) { case 0: trackingHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); break; case 1: trackingHandler->SetMode(mitk::TrackingDataHandler::MODE::PROBABILISTIC); break; default: trackingHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); } typedef itk::StreamlineTrackingFilter TrackerType; TrackerType::Pointer tracker = TrackerType::New(); if (m_Controls->m_InteractiveBox->isChecked()) { tracker->SetSeedPoints(m_SeedPoints); } else if (m_Controls->m_SeedImageBox->GetSelectedNode().IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_SeedImageBox->GetSelectedNode()->GetData()), mask); tracker->SetSeedImage(mask); } if (m_Controls->m_MaskImageBox->GetSelectedNode().IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_MaskImageBox->GetSelectedNode()->GetData()), mask); tracker->SetMaskImage(mask); } if (m_Controls->m_StopImageBox->GetSelectedNode().IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_StopImageBox->GetSelectedNode()->GetData()), mask); tracker->SetStoppingRegions(mask); } if (m_Controls->m_TissueImageBox->GetSelectedNode().IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_TissueImageBox->GetSelectedNode()->GetData()), mask); tracker->SetTissueImage(mask); tracker->SetSeedOnlyGm(m_Controls->m_SeedGmBox->isChecked()); } tracker->SetSeedsPerVoxel(m_Controls->m_SeedsPerVoxelBox->value()); tracker->SetStepSize(m_Controls->m_StepSizeBox->value()); //tracker->SetSamplingDistance(0.7); tracker->SetUseStopVotes(false); tracker->SetOnlyForwardSamples(false); tracker->SetAposterioriCurvCheck(false); tracker->SetMaxNumTracts(m_Controls->m_NumFibersBox->value()); tracker->SetNumberOfSamples(m_Controls->m_NumSamplesBox->value()); tracker->SetTrackingHandler(trackingHandler); tracker->SetAngularThreshold(m_Controls->m_AngularThresholdBox->value()); tracker->SetMinTractLength(m_Controls->m_MinTractLengthBox->value()); tracker->SetUseOutputProbabilityMap(m_Controls->m_OutputProbMap->isChecked() && !m_Controls->m_InteractiveBox->isChecked()); tracker->Update(); delete trackingHandler; if (m_Controls->m_InteractiveBox->isChecked()) { vtkSmartPointer fiberBundle = tracker->GetFiberPolyData(); if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("InteractiveFib"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle); fib->SetReferenceGeometry(dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()); if (m_Controls->m_ResampleFibersBox->isChecked()) fib->Compress(m_Controls->m_FiberErrorBox->value()); m_InteractiveNode->SetData(fib); } else if (!tracker->GetUseOutputProbabilityMap()) { vtkSmartPointer fiberBundle = tracker->GetFiberPolyData(); if (fiberBundle->GetNumberOfLines() == 0) { QMessageBox warnBox; warnBox.setWindowTitle("Warning"); warnBox.setText("No fiberbundle was generated!"); warnBox.setDetailedText("No fibers were generated using the parameters: \n\n" + m_Controls->m_FaThresholdLabel->text() + "\n" + m_Controls->m_AngularThresholdLabel->text() + "\n" + m_Controls->m_fLabel->text() + "\n" + m_Controls->m_gLabel->text() + "\n" + m_Controls->m_StepsizeLabel->text() + "\n" + m_Controls->m_MinTractLengthLabel->text() + "\n" + m_Controls->m_SeedsPerVoxelLabel->text() + "\n\nPlease check your parametersettings."); warnBox.setIcon(QMessageBox::Warning); warnBox.exec(); return; } mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle); fib->SetReferenceGeometry(dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()); if (m_Controls->m_ResampleFibersBox->isChecked()) fib->Compress(m_Controls->m_FiberErrorBox->value()); fib->ColorFibersByOrientation(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name("FiberBundle_"); name += m_InputImageNodes.at(0)->GetName().c_str(); name += "_Streamline"; node->SetName(name.toStdString()); GetDataStorage()->Add(node, m_InputImageNodes.at(0)); } else { TrackerType::ItkDoubleImgType::Pointer outImg = tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name("ProbabilityMap_"); name += m_InputImageNodes.at(0)->GetName().c_str(); node->SetName(name.toStdString()); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::JET_TRANSPARENT); mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New(); lut_prop->SetLookupTable(lut); node->SetProperty("LookupTable", lut_prop); node->SetProperty("opacity", mitk::FloatProperty::New(0.5)); GetDataStorage()->Add(node, m_InputImageNodes.at(0)); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui index 96b98a3cdf..e1660a9ab8 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui @@ -1,765 +1,771 @@ QmitkStreamlineTrackingViewControls 0 0 358 - 779 + 878 0 0 QmitkTemplate 0 0 3 3 Please Select Input Data Only track insida mask area. Mask Image: Fibers that enter a region defined in this image will stop immediately. QComboBox::AdjustToMinimumContentsLength - If an image is selected, the stopping criterion is not calculated from the input image but instead the selected image is used. QComboBox::AdjustToMinimumContentsLength - Binary seed ROI. If not specified, the whole image area is seeded. Seed Image: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Seed points are only placed inside the mask image. QComboBox::AdjustToMinimumContentsLength - Only track insida mask area. Stop Image: Input DTI Tensor/Peak/ODF Image: Only track insida mask area. FA/GFA Image: Tractography is only performed inside the mask image. Fibers that leave the mask image are stopped. QComboBox::AdjustToMinimumContentsLength - Only track insida mask area. Tissue Image: Tissue label image needed for gray matter seeding (WM=3, GM=1). Use e.g. MRtrix 5ttgen to generate such a label image. QComboBox::AdjustToMinimumContentsLength - false Start Tractography 0 0 Parameters Mode: Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. Deterministic Probabilistic Seeds per Voxel: Number of seed points placed in each voxel. 1 9999999 Max. num. fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed. 999999999 Cutoff: Threshold on peak magnitude, FA, GFA, ... 5 1.000000000000000 0.100000000000000 0.100000000000000 Qt::Horizontal QSizePolicy::Fixed 200 0 Advanced Paramaters Step Size: Step size (in voxels) 2 0.010000000000000 10.000000000000000 0.100000000000000 0.500000000000000 Angular Threshold: Default: 90° * step_size -1 90 1 -1 Min. Tract Length: Shorter fibers are discarded. + + Minimum fiber length (in mm) + 1 999.000000000000000 1.000000000000000 20.000000000000000 f parameter of tensor tractography. f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). f: f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 1.000000000000000 g: f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 0.000000000000000 Flip directions: QFrame::NoFrame QFrame::Raised 0 0 0 0 Internally flips progression directions. This might be necessary depending on the input data. x Internally flips progression directions. This might be necessary depending on the input data. y Internally flips progression directions. This might be necessary depending on the input data. z Neighborhood Samples: Number of neighborhood samples that are used to determine the next fiber progression direction. 50 Resample fibers using the specified error constraint. Compress Fibers true Qt::StrongFocus Lossy fiber compression. Recommended for large tractograms. Maximum error in mm. 3 10.000000000000000 0.010000000000000 0.100000000000000 If false, nearest neighbor interpolation is used. Enable Trilinear Interpolation true Requires tissue image. - Enable gray matter seeding + Enable Gray Matter Seeding false - Min-max normalize ODFs + Min-max Normalize ODFs true Output probability map instead of tractogram. - Output probability map + Output Probability Map false Qt::Vertical QSizePolicy::Expanding 20 220 0 0 - Interactive Tracking + Interactive Tractography Radius: false + + Dynamically pick seed location by click into image. + - Enable interactive tracking + Enable Interactive Tractography Num. Seeds: Number of seed points normally distributed around selected position. 1 9999999 50 - Seedpoints are normally distributed within a sphere centered at the selected position with the specified radius. + Seedpoints are normally distributed within a sphere centered at the selected position with the specified radius (in mm). 2 50.000000000000000 0.100000000000000 2.500000000000000 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h