diff --git a/Modules/DiffusionCore/Rendering/mitkFiberBundleMapper2D.cpp b/Modules/DiffusionCore/Rendering/mitkFiberBundleMapper2D.cpp index a2332fa..d64a0c3 100644 --- a/Modules/DiffusionCore/Rendering/mitkFiberBundleMapper2D.cpp +++ b/Modules/DiffusionCore/Rendering/mitkFiberBundleMapper2D.cpp @@ -1,335 +1,336 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 "mitkFiberBundleMapper2D.h" #include "mitkBaseRenderer.h" #include "mitkDataNode.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include class vtkShaderCallback : public vtkCommand { public: static vtkShaderCallback *New() { return new vtkShaderCallback; } mitk::BaseRenderer *renderer; mitk::DataNode *node; void Execute(vtkObject *, unsigned long, void*cbo) override { vtkShaderProgram *program = reinterpret_cast(cbo); float fiberOpacity; bool fiberFading = false; float fiberThickness = 0.0; node->GetOpacity(fiberOpacity, nullptr); node->GetFloatProperty("Fiber2DSliceThickness", fiberThickness); node->GetBoolProperty("Fiber2DfadeEFX", fiberFading); program->SetUniformf("fiberOpacity", fiberOpacity); program->SetUniformi("fiberFadingON", fiberFading); program->SetUniformf("fiberThickness", fiberThickness); // if (this->renderer) // { // //get information about current position of views // mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); // mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); // //generate according cutting planes based on the view position // float planeNormal[3]; // planeNormal[0] = planeGeo->GetNormal()[0]; // planeNormal[1] = planeGeo->GetNormal()[1]; // planeNormal[2] = planeGeo->GetNormal()[2]; // float tmp1 = planeGeo->GetOrigin()[0] * planeNormal[0]; // float tmp2 = planeGeo->GetOrigin()[1] * planeNormal[1]; // float tmp3 = planeGeo->GetOrigin()[2] * planeNormal[2]; // float odotn = tmp1 + tmp2 + tmp3; // float a[4]; // for (int i = 0; i < 3; ++i) // a[i] = planeNormal[i]; // a[3] = odotn; // MITK_INFO << "IN CALLBACK"; // MITK_INFO << planeGeo->GetNormal(); // MITK_INFO << planeGeo->GetOrigin(); // for (int i = 0; i < 4; ++i) // MITK_INFO << a[i]; // program->SetUniform4f("slicingPlane", a); // } } vtkShaderCallback() { this->renderer = nullptr; } }; mitk::FiberBundleMapper2D::FiberBundleMapper2D() : m_LineWidth(1) { m_lut = vtkSmartPointer::New(); m_lut->Build(); } mitk::FiberBundleMapper2D::~FiberBundleMapper2D() { } mitk::FiberBundle* mitk::FiberBundleMapper2D::GetInput() { return dynamic_cast< mitk::FiberBundle * > ( GetDataNode()->GetData() ); } void mitk::FiberBundleMapper2D::Update(mitk::BaseRenderer * renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); //check if updates occured in the node or on the display FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); //set renderer independent shader properties const DataNode::Pointer node = this->GetDataNode(); float thickness = 2.0; if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness)) MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR"; bool fiberfading = false; if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading)) MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR"; mitk::FiberBundle* fiberBundle = this->GetInput(); if (fiberBundle==nullptr) return; - int lineWidth = 1.0; - node->GetIntProperty("LineWidth", lineWidth); - if (m_LineWidth!=lineWidth) - { - m_LineWidth = lineWidth; - fiberBundle->RequestUpdate2D(); - } - vtkProperty *property = localStorage->m_Actor->GetProperty(); property->SetLighting(false); if ( localStorage->m_LastUpdateTimeGetCurrentWorldPlaneGeometryUpdateTime() || localStorage->m_LastUpdateTimeGetUpdateTime2D() ) { this->UpdateShaderParameter(renderer); this->GenerateDataForRenderer( renderer ); } } void mitk::FiberBundleMapper2D::UpdateShaderParameter(mitk::BaseRenderer *) { // see new vtkShaderCallback } // vtkActors and Mappers are feeded here void mitk::FiberBundleMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { mitk::FiberBundle* fiberBundle = this->GetInput(); //the handler of local storage gets feeded in this method with requested data for related renderwindow FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); mitk::DataNode* node = this->GetDataNode(); if (node == nullptr) return; vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); if (fiberPolyData == nullptr) return; fiberPolyData->GetPointData()->AddArray(fiberBundle->GetFiberColors()); localStorage->m_Mapper->ScalarVisibilityOn(); localStorage->m_Mapper->SetScalarModeToUsePointFieldData(); // localStorage->m_Mapper->SetLookupTable(m_lut); //apply the properties after the slice was set // localStorage->m_Actor->GetProperty()->SetOpacity(0.999); localStorage->m_Mapper->SelectColorArray("FIBER_COLORS"); localStorage->m_Mapper->SetInputData(fiberPolyData); float d = 1.0; node->GetFloatProperty("Fiber2DSliceThickness", d); mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); const Point3D &origin = planeGeo->GetOrigin(); const Vector3D &normal = planeGeo->GetNormal(); vtkSmartPointer plane1 = vtkSmartPointer::New(); plane1->SetOrigin(origin[0]+normal[0]*d, origin[1]+normal[1]*d, origin[2]+normal[2]*d); // plane1->SetOrigin(origin[0], origin[1], origin[2]); plane1->SetNormal(-normal[0], -normal[1], -normal[2]); vtkSmartPointer plane2 = vtkSmartPointer::New(); plane2->SetOrigin(origin[0]-normal[0]*d, origin[1]-normal[1]*d, origin[2]-normal[2]*d); plane2->SetNormal(normal[0], normal[1], normal[2]); vtkSmartPointer planes = vtkSmartPointer::New();; planes->AddItem(plane1); planes->AddItem(plane2); localStorage->m_Mapper->SetClippingPlanes(planes); // localStorage->m_Actor->GetShaderProperty()->SetVertexShaderCode( // "//VTK::System::Dec\n" // "attribute vec4 vertexMC;\n" // "//VTK::Normal::Dec\n" // "uniform mat4 MCDCMatrix;\n" // "//VTK::Color::Dec\n" // "varying vec4 positionWorld;\n" // "varying vec4 colorVertex;\n" // "void main(void)\n" // "{\n" // " colorVertex = scalarColor;\n" // " positionWorld = vertexMC;\n" // " gl_Position = MCDCMatrix * vertexMC;\n" // "}\n" // ); // localStorage->m_Actor->GetShaderProperty()->SetFragmentShaderCode( // "//VTK::System::Dec\n" // always start with this line // "//VTK::Output::Dec\n" // always have this line in your FS // "uniform vec4 slicingPlane;\n" // "uniform float fiberThickness;\n" // "uniform int fiberFadingON;\n" // "uniform float fiberOpacity;\n" // "varying vec4 positionWorld;\n" // "varying vec4 colorVertex;\n" // "out vec4 out_Color;\n" // "void main(void)\n" // "{\n" // " float r1 = dot(positionWorld.xyz, slicingPlane.xyz) - slicingPlane.w;\n" // " if (abs(r1) >= fiberThickness)\n" // " discard;\n" // " if (fiberFadingON != 0)\n" // " {\n" // " float x = (r1 + fiberThickness) / (fiberThickness*2.0);\n" // " x = 1.0 - x;\n" // " out_Color = vec4(colorVertex.xyz*x, fiberOpacity);\n" // " }\n" // " else{\n" // " out_Color = vec4(colorVertex.xyz, fiberOpacity);\n" // " }\n" // "}\n" // ); // localStorage->m_Actor->GetShaderProperty()->AddVertexShaderReplacement("//VTK::TCoord::Dec", true, "uniform vec4 slicingPlane;\n" // "out float fade_dist;", true); // localStorage->m_Actor->GetShaderProperty()->AddVertexShaderReplacement("//VTK::TCoord::Impl", true, "fade_dist = abs(dot(vertexMC.xyz, slicingPlane.xyz) - slicingPlane.w);", true); // localStorage->m_Actor->GetShaderProperty()->AddFragmentShaderReplacement("//VTK::TCoord::Dec", true, "uniform float fiberThickness;\n" // "in float fade_dist;\n" // "uniform int fiberFadingON;", true); //// std::string colorImpl = " if (fade_dist > fiberThickness) discard;\n" //// " vec3 ambientColor = ambientIntensity * vertexColorVSOutput.rgb;\n" //// " vec3 diffuseColor = diffuseIntensity * vertexColorVSOutput.rgb;\n" //// " float opacity = opacityUniform * vertexColorVSOutput.a;\n"; ////// " if (fiberFadingON != 0)\n" ////// " opacity = opacity*fade_dist;\n"; //// localStorage->m_Actor->GetShaderProperty()->AddFragmentShaderReplacement("//VTK::Color::Impl", true, colorImpl, true); // localStorage->m_Actor->GetShaderProperty()->AddFragmentShaderReplacement("//VTK::Clip::Impl", true, "for (int planeNum = 0; planeNum < numClipPlanes; planeNum++)\n" // " {\n" // " if (abs(clipDistancesVSOutput[planeNum]) > fiberThickness) discard;\n" // " }\n", true); // vtkSmartPointer myCallback = vtkSmartPointer::New(); // myCallback->renderer = renderer; // myCallback->node = this->GetDataNode(); // localStorage->m_Mapper->AddObserver(vtkCommand::UpdateShaderEvent,myCallback); localStorage->m_Actor->SetMapper(localStorage->m_Mapper); + + int lineWidth = 0; + node->GetIntProperty("shape.linewidth", lineWidth); + if (m_LineWidth!=lineWidth) + { + m_LineWidth = lineWidth; + fiberBundle->RequestUpdate2D(); + } + localStorage->m_Actor->GetProperty()->SetLineWidth(m_LineWidth); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } vtkProp* mitk::FiberBundleMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { this->Update(renderer); return m_LocalStorageHandler.GetLocalStorage(renderer)->m_Actor; } void mitk::FiberBundleMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { Superclass::SetDefaultProperties(node, renderer, overwrite); // node->SetProperty("shader",mitk::ShaderProperty::New("mitkShaderFiberClipping")); //add other parameters to propertylist node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(1.0f), renderer, overwrite ); node->AddProperty( "Fiber2DfadeEFX", mitk::BoolProperty::New(true), renderer, overwrite ); node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite); } mitk::FiberBundleMapper2D::FBXLocalStorage::FBXLocalStorage() { m_Actor = vtkSmartPointer::New(); m_Mapper = vtkSmartPointer::New(); } 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 09d0d27..0f36d5a 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 @@ -1,1218 +1,1219 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include // VTK #include #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; QmitkStreamlineTrackingWorker::QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view) : m_View(view) { } void QmitkStreamlineTrackingWorker::run() { m_View->m_Tracker->Update(); m_View->m_TrackingThread.quit(); } QmitkStreamlineTrackingView::QmitkStreamlineTrackingView() : m_TrackingWorker(this) , m_Controls(nullptr) , m_FirstTensorProbRun(true) , m_FirstInteractiveRun(true) , m_TrackingHandler(nullptr) , m_ThreadIsRunning(false) , m_DeleteTrackingHandler(false) , m_Visible(false) , m_LastPrior(nullptr) , m_TrackingPriorHandler(nullptr) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } // Destructor QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); m_TrackingThread.wait(); } 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_FaImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_SeedImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_TargetImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_PriorImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_StopImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ForestSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ExclusionImageSelectionWidget->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPeakImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isTractographyForest = 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_ForestSelectionWidget->SetNodePredicate(isTractographyForest); m_Controls->m_FaImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); m_Controls->m_FaImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_FaImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_SeedImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_SeedImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_SeedImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_MaskImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_MaskImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_MaskImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_StopImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_StopImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_StopImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_TargetImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_TargetImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_TargetImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_PriorImageSelectionWidget->SetNodePredicate( isPeakImagePredicate ); m_Controls->m_PriorImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_PriorImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_ExclusionImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_ExclusionImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_ExclusionImageSelectionWidget->SetSelectionIsOptional(true); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->m_SaveParametersButton, SIGNAL(clicked()), this, SLOT(SaveParameters()) ); connect( m_Controls->m_LoadParametersButton, SIGNAL(clicked()), this, SLOT(LoadParameters()) ); connect( m_Controls->commandLinkButton_2, SIGNAL(clicked()), this, SLOT(StopTractography()) ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_InteractiveBox, SIGNAL(stateChanged(int)), this, SLOT(ToggleInteractive()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); connect( m_Controls->m_FaImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::DeleteTrackingHandler ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DeleteTrackingHandler()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OutputStyleSwitched()) ); connect( m_Controls->m_SeedImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_TargetImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_PriorImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ExclusionImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_MaskImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_FaImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ForestSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::ForestSwitched ); connect( m_Controls->m_ForestSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_SeedsPerVoxelBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumFibersBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ScalarThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_OdfCutoffBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StepSizeBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SamplingDistanceBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_AngularThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MinTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaxTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_fBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_gBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumSamplesBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SeedRadiusBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_NumSeedsBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SharpenOdfsBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_InterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaskInterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FrontalSamplesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopVotesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_LoopCheckBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_TrialsPerSeedBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_EpConstraintsBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PeakJitterBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); + connect( m_Controls->m_SecondOrderBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); m_Controls->m_SharpenOdfsBox->editingFinished(); m_Controls->m_SeedsPerVoxelBox->editingFinished(); m_Controls->m_NumFibersBox->editingFinished(); m_Controls->m_ScalarThresholdBox->editingFinished(); m_Controls->m_OdfCutoffBox->editingFinished(); m_Controls->m_StepSizeBox->editingFinished(); m_Controls->m_SamplingDistanceBox->editingFinished(); m_Controls->m_AngularThresholdBox->editingFinished(); m_Controls->m_MinTractLengthBox->editingFinished(); m_Controls->m_MaxTractLengthBox->editingFinished(); m_Controls->m_fBox->editingFinished(); m_Controls->m_gBox->editingFinished(); m_Controls->m_NumSamplesBox->editingFinished(); m_Controls->m_SeedRadiusBox->editingFinished(); m_Controls->m_NumSeedsBox->editingFinished(); m_Controls->m_LoopCheckBox->editingFinished(); m_Controls->m_TrialsPerSeedBox->editingFinished(); m_Controls->m_PeakJitterBox->editingFinished(); StartStopTrackingGui(false); } m_ParameterFile = QDir::currentPath()+"/param.stp"; UpdateGui(); } void QmitkStreamlineTrackingView::ParametersToGui(mitk::StreamlineTractographyParameters& params) { m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm); m_Controls->m_NumSeedsBox->setValue(params.m_NumInteractiveSeeds); m_Controls->m_InteractiveBox->setChecked(params.m_EnableInteractive); m_Controls->m_ResampleFibersBox->setChecked(params.m_CompressFibers); m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm); m_Controls->m_NumFibersBox->setValue(params.m_MaxNumFibers); m_Controls->m_ScalarThresholdBox->setValue(params.m_Cutoff); m_Controls->m_fBox->setValue(params.m_F); m_Controls->m_gBox->setValue(params.m_G); m_Controls->m_OdfCutoffBox->setValue(params.m_OdfCutoff); m_Controls->m_SharpenOdfsBox->setValue(params.m_SharpenOdfs); m_Controls->m_PriorWeightBox->setValue(params.m_Weight); m_Controls->m_PriorAsMaskBox->setChecked(params.m_RestrictToPrior); m_Controls->m_NewDirectionsFromPriorBox->setChecked(params.m_NewDirectionsFromPrior); m_Controls->m_PriorFlipXBox->setChecked(params.m_PriorFlipX); m_Controls->m_PriorFlipYBox->setChecked(params.m_PriorFlipY); m_Controls->m_PriorFlipZBox->setChecked(params.m_PriorFlipZ); m_Controls->m_FlipXBox->setChecked(params.m_FlipX); m_Controls->m_FlipYBox->setChecked(params.m_FlipY); m_Controls->m_FlipZBox->setChecked(params.m_FlipZ); m_Controls->m_InterpolationBox->setChecked(params.m_InterpolateTractographyData); m_Controls->m_MaskInterpolationBox->setChecked(params.m_InterpolateRoiImages); m_Controls->m_SeedsPerVoxelBox->setValue(params.m_SeedsPerVoxel); m_Controls->m_StepSizeBox->setValue(params.GetStepSizeVox()); m_Controls->m_SamplingDistanceBox->setValue(params.GetSamplingDistanceVox()); m_Controls->m_StopVotesBox->setChecked(params.m_StopVotes); m_Controls->m_FrontalSamplesBox->setChecked(params.m_OnlyForwardSamples); m_Controls->m_TrialsPerSeedBox->setValue(params.m_TrialsPerSeed); m_Controls->m_NumSamplesBox->setValue(params.m_NumSamples); m_Controls->m_LoopCheckBox->setValue(params.GetLoopCheckDeg()); m_Controls->m_AngularThresholdBox->setValue(params.GetAngularThresholdDeg()); m_Controls->m_MinTractLengthBox->setValue(params.m_MinTractLengthMm); m_Controls->m_MaxTractLengthBox->setValue(params.m_MaxTractLengthMm); m_Controls->m_OutputProbMap->setChecked(params.m_OutputProbMap); m_Controls->m_FixSeedBox->setChecked(params.m_FixRandomSeed); m_Controls->m_SecondOrderBox->setChecked(params.m_SecondOrder); m_Controls->m_PeakJitterBox->setValue(params.m_PeakJitter); switch (params.m_Mode) { case mitk::TrackingDataHandler::MODE::DETERMINISTIC: m_Controls->m_ModeBox->setCurrentIndex(0); break; case mitk::TrackingDataHandler::MODE::PROBABILISTIC: m_Controls->m_ModeBox->setCurrentIndex(1); break; } switch (params.m_EpConstraints) { case itk::StreamlineTrackingFilter::EndpointConstraints::NONE: m_Controls->m_EpConstraintsBox->setCurrentIndex(0); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(1); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF: m_Controls->m_EpConstraintsBox->setCurrentIndex(2); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(3); break; case itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(4); break; case itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(5); break; case itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(6); break; } } std::shared_ptr QmitkStreamlineTrackingView::GetParametersFromGui() { std::shared_ptr params = std::make_shared(); // NOT IN GUI // unsigned int m_NumPreviousDirections = 1; // bool m_AvoidStop = true; // bool m_RandomSampling = false; // float m_DeflectionMod = 1.0; // bool m_ApplyDirectionMatrix = false; // NOT IN GUI BUT AUTOMATICALLY SET if (!m_InputImageNodes.empty()) { float min_sp = 999; auto spacing = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetSpacing(); if (spacing[0] < min_sp) min_sp = spacing[0]; if (spacing[1] < min_sp) min_sp = spacing[1]; if (spacing[2] < min_sp) min_sp = spacing[2]; params->m_Compression = min_sp/10; } params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value(); params->m_NumInteractiveSeeds = m_Controls->m_NumSeedsBox->value(); params->m_EnableInteractive = m_Controls->m_InteractiveBox->isChecked(); params->m_CompressFibers = m_Controls->m_ResampleFibersBox->isChecked(); params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value(); params->m_MaxNumFibers = m_Controls->m_NumFibersBox->value(); params->m_Cutoff = static_cast(m_Controls->m_ScalarThresholdBox->value()); params->m_F = static_cast(m_Controls->m_fBox->value()); params->m_G = static_cast(m_Controls->m_gBox->value()); params->m_OdfCutoff = static_cast(m_Controls->m_OdfCutoffBox->value()); params->m_SharpenOdfs = m_Controls->m_SharpenOdfsBox->value(); params->m_Weight = static_cast(m_Controls->m_PriorWeightBox->value()); params->m_RestrictToPrior = m_Controls->m_PriorAsMaskBox->isChecked(); params->m_NewDirectionsFromPrior = m_Controls->m_NewDirectionsFromPriorBox->isChecked(); params->m_PriorFlipX = m_Controls->m_PriorFlipXBox->isChecked(); params->m_PriorFlipY = m_Controls->m_PriorFlipYBox->isChecked(); params->m_PriorFlipZ = m_Controls->m_PriorFlipZBox->isChecked(); params->m_FlipX = m_Controls->m_FlipXBox->isChecked(); params->m_FlipY = m_Controls->m_FlipYBox->isChecked(); params->m_FlipZ = m_Controls->m_FlipZBox->isChecked(); params->m_InterpolateTractographyData = m_Controls->m_InterpolationBox->isChecked(); params->m_InterpolateRoiImages = m_Controls->m_MaskInterpolationBox->isChecked(); params->m_SeedsPerVoxel = m_Controls->m_SeedsPerVoxelBox->value(); params->SetStepSizeVox(m_Controls->m_StepSizeBox->value()); params->SetSamplingDistanceVox(m_Controls->m_SamplingDistanceBox->value()); params->m_StopVotes = m_Controls->m_StopVotesBox->isChecked(); params->m_OnlyForwardSamples = m_Controls->m_FrontalSamplesBox->isChecked(); params->m_TrialsPerSeed = m_Controls->m_TrialsPerSeedBox->value(); params->m_NumSamples = m_Controls->m_NumSamplesBox->value(); params->SetLoopCheckDeg(m_Controls->m_LoopCheckBox->value()); params->SetAngularThresholdDeg(m_Controls->m_AngularThresholdBox->value()); params->m_MinTractLengthMm = m_Controls->m_MinTractLengthBox->value(); params->m_MaxTractLengthMm = m_Controls->m_MaxTractLengthBox->value(); params->m_OutputProbMap = m_Controls->m_OutputProbMap->isChecked(); params->m_FixRandomSeed = m_Controls->m_FixSeedBox->isChecked(); params->m_SecondOrder = m_Controls->m_SecondOrderBox->isChecked(); params->m_PeakJitter = static_cast(m_Controls->m_PeakJitterBox->value()); switch (m_Controls->m_ModeBox->currentIndex()) { case 0: params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC; break; case 1: params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC; break; default: params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC; } switch (m_Controls->m_EpConstraintsBox->currentIndex()) { case 0: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NONE; break; case 1: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET; break; case 2: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF; break; case 3: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET; break; case 4: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET; break; case 5: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET; break; case 6: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET; break; } return params; } void QmitkStreamlineTrackingView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Tractography Parameters"), m_ParameterFile, tr("Streamline Tractography Parameters (*.stp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; auto params = GetParametersFromGui(); params->SaveParameters(m_ParameterFile.toStdString()); } void QmitkStreamlineTrackingView::LoadParameters() { QString filename = QFileDialog::getOpenFileName( 0, tr("Load Tractography Parameters"), m_ParameterFile, tr("Streamline Tractography Parameters (*.stp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; mitk::StreamlineTractographyParameters params; params.LoadParameters(m_ParameterFile.toStdString()); ParametersToGui(params); } void QmitkStreamlineTrackingView::StopTractography() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); } void QmitkStreamlineTrackingView::TimerUpdate() { if (m_Tracker.IsNull()) return; QString status_text(m_Tracker->GetStatusText().c_str()); m_Controls->m_StatusTextBox->setText(status_text); } void QmitkStreamlineTrackingView::BeforeThread() { m_TrackingTimer->start(1000); } void QmitkStreamlineTrackingView::AfterThread() { auto params = m_Tracker->GetParameters(); m_TrackingTimer->stop(); if (!params->m_OutputProbMap) { vtkSmartPointer fiberBundle = m_Tracker->GetFiberPolyData(); if (!m_Controls->m_InteractiveBox->isChecked() && fiberBundle->GetNumberOfLines() == 0) { QMessageBox warnBox; warnBox.setWindowTitle("Warning"); warnBox.setText("No fiberbundle was generated!"); warnBox.setDetailedText("No fibers were generated using the chosen parameters. Typical reasons are:\n\n- Cutoff too high. Some images feature very low FA/GFA/peak size. Try to lower this parameter.\n- Angular threshold too strict. Try to increase this parameter.\n- A small step sizes also means many steps to go wrong. Especially in the case of probabilistic tractography. Try to adjust the angular threshold.\n- In case of probabilistic tractography, try to increase the parameter for ODF sharpening (for ODF and tensor tractography) or decrease the peak jitter (for peak tracking)."); warnBox.setIcon(QMessageBox::Warning); warnBox.exec(); if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); return; } mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle); fib->SetTrackVisHeader(dynamic_cast(m_ParentNode->GetData())->GetGeometry()); if (params->m_CompressFibers && fiberBundle->GetNumberOfLines()>0) fib->Compress(params->m_Compression); fib->ColorFibersByOrientation(); m_Tracker->SetDicomProperties(fib); mitk::DiffusionPropertyHelper::CopyDICOMProperties(m_ParentNode->GetData(), fib); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(fib); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name("FiberBundle_"); name += m_ParentNode->GetName().c_str(); name += "_Streamline"; node->SetName(name.toStdString()); node->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); GetDataStorage()->Add(node, m_ParentNode); } } else { TrackerType::ItkDoubleImgType::Pointer outImg = m_Tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); mitk::DiffusionPropertyHelper::CopyDICOMProperties(m_ParentNode->GetData(), img); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(img); 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); m_InteractiveNode->SetProperty("LookupTable", lut_prop); m_InteractiveNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name("ProbabilityMap_"); name += m_ParentNode->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_ParentNode); } } if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); } void QmitkStreamlineTrackingView::InteractiveSeedChanged(bool posChanged) { if(!CheckAndStoreLastParams(sender()) && !posChanged) return; if (m_ThreadIsRunning || !m_Visible) return; if (!posChanged && (!m_Controls->m_InteractiveBox->isChecked() || !m_Controls->m_ParamUpdateBox->isChecked()) ) return; 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); } m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,0,0)); DoFiberTracking(); } bool QmitkStreamlineTrackingView::CheckAndStoreLastParams(QObject* obj) { if (obj!=nullptr) { std::string new_val = ""; if(qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else if (qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else return true; if (m_LastTractoParams.find(obj->objectName())==m_LastTractoParams.end()) { m_LastTractoParams[obj->objectName()] = new_val; return false; } else if (m_LastTractoParams.at(obj->objectName()) != new_val) { m_LastTractoParams[obj->objectName()] = new_val; return true; } else if (m_LastTractoParams.at(obj->objectName()) == new_val) return false; } return true; } void QmitkStreamlineTrackingView::OnParameterChanged() { UpdateGui(); if(!CheckAndStoreLastParams(sender())) return; if (m_Controls->m_InteractiveBox->isChecked() && m_Controls->m_ParamUpdateBox->isChecked()) DoFiberTracking(); } void QmitkStreamlineTrackingView::ToggleInteractive() { UpdateGui(); m_Controls->m_SeedsPerVoxelBox->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedsPerVoxelLabel->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedImageSelectionWidget->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->label_6->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); if ( m_Controls->m_InteractiveBox->isChecked() ) { if (m_FirstInteractiveRun) { QMessageBox::information(nullptr, "Information", "Place and move a spherical seed region anywhere in the image by left-clicking and dragging. If the seed region is colored red, tracking is in progress. If the seed region is colored white, tracking is finished.\nPlacing the seed region for the first time in a newly selected dataset might cause a short delay, since the tracker needs to be initialized."); m_FirstInteractiveRun = false; } QApplication::setOverrideCursor(Qt::PointingHandCursor); QApplication::processEvents(); 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); m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } else { QApplication::restoreOverrideCursor(); QApplication::processEvents(); m_InteractiveNode = nullptr; m_InteractivePointSetNode = nullptr; m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); disconnect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } } void QmitkStreamlineTrackingView::Activated() { } void QmitkStreamlineTrackingView::Deactivated() { } void QmitkStreamlineTrackingView::Visible() { m_Visible = true; } void QmitkStreamlineTrackingView::Hidden() { m_Visible = false; m_Controls->m_InteractiveBox->setChecked(false); ToggleInteractive(); } void QmitkStreamlineTrackingView::OnSliceChanged() { InteractiveSeedChanged(true); } void QmitkStreamlineTrackingView::SetFocus() { } void QmitkStreamlineTrackingView::DeleteTrackingHandler() { if (!m_ThreadIsRunning && m_TrackingHandler != nullptr) { if (m_TrackingPriorHandler != nullptr) { delete m_TrackingPriorHandler; m_TrackingPriorHandler = nullptr; } delete m_TrackingHandler; m_TrackingHandler = nullptr; m_DeleteTrackingHandler = false; m_LastPrior = nullptr; } else if (m_ThreadIsRunning) { m_DeleteTrackingHandler = true; } } void QmitkStreamlineTrackingView::ForestSwitched() { DeleteTrackingHandler(); } void QmitkStreamlineTrackingView::OutputStyleSwitched() { if (m_InteractiveNode.IsNotNull()) GetDataStorage()->Remove(m_InteractiveNode); m_InteractiveNode = nullptr; } void QmitkStreamlineTrackingView::OnSelectionChanged( berry::IWorkbenchPart::Pointer , const QList& nodes ) { std::vector< mitk::DataNode::Pointer > last_nodes = m_InputImageNodes; m_InputImageNodes.clear(); m_AdditionalInputImages.clear(); bool retrack = false; for( auto node : nodes ) { if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData()))) { m_InputImageNodes.push_back(node); retrack = true; } else { mitk::Image* img = dynamic_cast(node->GetData()); if (img!=nullptr && img->GetDimension()==3) m_AdditionalInputImages.push_back(dynamic_cast(node->GetData())); } } } // sometimes the OnSelectionChanged event is sent twice and actually no selection has changed for the first event. We need to catch that. if (last_nodes.size() == m_InputImageNodes.size()) { bool same_nodes = true; for (unsigned int i=0; im_TensorImageLabel->setText("select in data-manager"); m_Controls->m_fBox->setEnabled(false); m_Controls->m_fLabel->setEnabled(false); m_Controls->m_gBox->setEnabled(false); m_Controls->m_gLabel->setEnabled(false); m_Controls->m_FaImageSelectionWidget->setEnabled(true); m_Controls->mFaImageLabel->setEnabled(true); m_Controls->m_OdfCutoffBox->setEnabled(false); m_Controls->m_OdfCutoffLabel->setEnabled(false); m_Controls->m_SharpenOdfsBox->setEnabled(false); m_Controls->m_ForestSelectionWidget->setVisible(false); m_Controls->m_ForestLabel->setVisible(false); m_Controls->commandLinkButton->setEnabled(false); m_Controls->m_TrialsPerSeedBox->setEnabled(false); m_Controls->m_TrialsPerSeedLabel->setEnabled(false); m_Controls->m_TargetImageSelectionWidget->setEnabled(false); m_Controls->m_TargetImageLabel->setEnabled(false); m_Controls->m_PeakJitterBox->setEnabled(false); if (m_Controls->m_InteractiveBox->isChecked()) { m_Controls->m_InteractiveSeedingFrame->setVisible(true); m_Controls->m_StaticSeedingFrame->setVisible(false); m_Controls->commandLinkButton_2->setVisible(false); m_Controls->commandLinkButton->setVisible(false); } else { m_Controls->m_InteractiveSeedingFrame->setVisible(false); m_Controls->m_StaticSeedingFrame->setVisible(true); m_Controls->commandLinkButton_2->setVisible(m_ThreadIsRunning); m_Controls->commandLinkButton->setVisible(!m_ThreadIsRunning); } if (m_Controls->m_EpConstraintsBox->currentIndex()>0) { m_Controls->m_TargetImageSelectionWidget->setEnabled(true); m_Controls->m_TargetImageLabel->setEnabled(true); } // stuff that is only important for probabilistic tractography if (m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_TrialsPerSeedBox->setEnabled(true); m_Controls->m_TrialsPerSeedLabel->setEnabled(true); } if(!m_InputImageNodes.empty()) { if (m_InputImageNodes.size()>1) m_Controls->m_TensorImageLabel->setText( ( std::to_string(m_InputImageNodes.size()) + " images selected").c_str() ); else m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.at(0)->GetName().c_str()); m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked() && !m_ThreadIsRunning); m_Controls->m_ScalarThresholdBox->setEnabled(true); m_Controls->m_FaThresholdLabel->setEnabled(true); if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { if (m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_OdfCutoffBox->setEnabled(true); m_Controls->m_OdfCutoffLabel->setEnabled(true); m_Controls->m_SharpenOdfsBox->setEnabled(true); } else { m_Controls->m_fBox->setEnabled(true); m_Controls->m_fLabel->setEnabled(true); m_Controls->m_gBox->setEnabled(true); m_Controls->m_gLabel->setEnabled(true); } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { m_Controls->m_OdfCutoffBox->setEnabled(true); m_Controls->m_OdfCutoffLabel->setEnabled(true); m_Controls->m_SharpenOdfsBox->setEnabled(true); } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { m_Controls->m_ForestSelectionWidget->setVisible(true); m_Controls->m_ForestLabel->setVisible(true); m_Controls->m_ScalarThresholdBox->setEnabled(false); m_Controls->m_FaThresholdLabel->setEnabled(false); } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) && m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_PeakJitterBox->setEnabled(true); } } } void QmitkStreamlineTrackingView::StartStopTrackingGui(bool start) { m_ThreadIsRunning = start; if (!m_Controls->m_InteractiveBox->isChecked()) { m_Controls->commandLinkButton_2->setVisible(start); m_Controls->commandLinkButton->setVisible(!start); m_Controls->m_InteractiveBox->setEnabled(!start); m_Controls->m_StatusTextBox->setVisible(start); } } void QmitkStreamlineTrackingView::DoFiberTracking() { auto params = GetParametersFromGui(); if (m_InputImageNodes.empty()) { QMessageBox::information(nullptr, "Information", "Please select an input image in the datamaneger (tensor, ODF, peak or dMRI image)!"); return; } if (m_ThreadIsRunning || !m_Visible) return; if (m_Controls->m_InteractiveBox->isChecked() && m_SeedPoints.empty()) return; StartStopTrackingGui(true); m_Tracker = TrackerType::New(); if (params->m_EpConstraints == itk::StreamlineTrackingFilter::EndpointConstraints::NONE) m_Tracker->SetTargetRegions(nullptr); if( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { if (m_Controls->m_ModeBox->currentIndex()==1) { if (m_InputImageNodes.size()>1) { QMessageBox::information(nullptr, "Information", "Probabilistic tensor tractography is only implemented for single-tensor mode!"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); typedef itk::TensorImageToOdfImageFilter< float, float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(0)->GetData())) ); filter->Update(); dynamic_cast(m_TrackingHandler)->SetOdfImage(filter->GetOutput()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } dynamic_cast(m_TrackingHandler)->SetIsOdfFromTensor(true); } else { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerTensor(); for (unsigned int i=0; i(m_TrackingHandler)->AddTensorImage(mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(i)->GetData())).GetPointer()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetFaImage(itkImg); } } } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); if (dynamic_cast(m_InputImageNodes.at(0)->GetData())) dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromShImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); else dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromOdfImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { if ( m_Controls->m_ForestSelectionWidget->GetSelectedNode().IsNull() ) { QMessageBox::information(nullptr, "Information", "Not random forest for machine learning based tractography (raw dMRI tractography) selected. Did you accidentally select the raw diffusion-weighted image in the datamanager?"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { mitk::TractographyForest::Pointer forest = dynamic_cast(m_Controls->m_ForestSelectionWidget->GetSelectedNode()->GetData()); mitk::Image::Pointer dwi = dynamic_cast(m_InputImageNodes.at(0)->GetData()); std::vector< std::vector< ItkFloatImageType::Pointer > > additionalFeatureImages; additionalFeatureImages.push_back(std::vector< ItkFloatImageType::Pointer >()); for (auto img : m_AdditionalInputImages) { ItkFloatImageType::Pointer itkimg = ItkFloatImageType::New(); mitk::CastToItkImage(img, itkimg); additionalFeatureImages.at(0).push_back(itkimg); } bool forest_valid = false; if (forest->GetNumFeatures()>=100) { params->m_NumPreviousDirections = static_cast((forest->GetNumFeatures() - (100 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 100>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } else { params->m_NumPreviousDirections = static_cast((forest->GetNumFeatures() - (28 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 28>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } if (!forest_valid) { QMessageBox::information(nullptr, "Information", "Random forest is invalid. The forest signatue does not match the parameters of TrackingHandlerRandomForest."); StartStopTrackingGui(false); return; } } } else { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingHandler)->SetPeakImage(mitk::convert::GetItkPeakFromPeakImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); } } if (m_Controls->m_InteractiveBox->isChecked()) { m_Tracker->SetSeedPoints(m_SeedPoints); } else if (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_SeedImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetSeedImage(mask); } if (m_Controls->m_MaskImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_MaskImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetMaskImage(mask); } if (m_Controls->m_StopImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_StopImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetStoppingRegions(mask); } if (m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_TargetImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetTargetRegions(mask); } if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNotNull()) { auto prior_params = GetParametersFromGui(); if (m_LastPrior!=m_Controls->m_PriorImageSelectionWidget->GetSelectedNode() || m_TrackingPriorHandler==nullptr) { typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(dynamic_cast(m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetData())); caster->SetCopyMemFlag(true); caster->Update(); mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput(); m_TrackingPriorHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingPriorHandler)->SetPeakImage(itkImg); m_LastPrior = m_Controls->m_PriorImageSelectionWidget->GetSelectedNode(); } prior_params->m_FlipX = m_Controls->m_PriorFlipXBox->isChecked(); prior_params->m_FlipY = m_Controls->m_PriorFlipYBox->isChecked(); prior_params->m_FlipZ = m_Controls->m_PriorFlipZBox->isChecked(); m_TrackingPriorHandler->SetParameters(prior_params); m_Tracker->SetTrackingPriorHandler(m_TrackingPriorHandler); } else if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNull()) m_Tracker->SetTrackingPriorHandler(nullptr); if (m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetExclusionRegions(mask); } if (params->m_EpConstraints!=itk::StreamlineTrackingFilter::EndpointConstraints::NONE && m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) { QMessageBox::information(nullptr, "Error", "Endpoint constraints are used but no target image is set!"); StartStopTrackingGui(false); return; } else if (params->m_EpConstraints==itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET && (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNull()|| m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) ) { QMessageBox::information(nullptr, "Error", "Endpoint constraint EPS_IN_SEED_AND_TARGET is used but no target or no seed image is set!"); StartStopTrackingGui(false); return; } float min_sp = 999; auto spacing = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetSpacing(); if (spacing[0] < min_sp) min_sp = spacing[0]; if (spacing[1] < min_sp) min_sp = spacing[1]; if (spacing[2] < min_sp) min_sp = spacing[2]; params->m_Compression = min_sp/10; // float max_size = 0; // for (int i=0; i<3; ++i) // if (dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i)>max_size) // max_size = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i); // if (params->m_MinTractLengthMm >= max_size) // { // MITK_INFO << "Max. image size: " << max_size << "mm"; // MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; // QMessageBox::information(nullptr, "Error", "Minimum tract length exceeds the maximum image extent! Recommended value is about 1/10 of the image extent."); // StartStopTrackingGui(false); // return; // } // else if (params->m_MinTractLengthMm > max_size/10) // { // MITK_INFO << "Max. image size: " << max_size << "mm"; // MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; // MITK_WARN << "Minimum tract length is larger than 1/10 the maximum image extent! Decrease recommended."; // } m_Tracker->SetParameters(params); m_Tracker->SetTrackingHandler(m_TrackingHandler); m_Tracker->SetVerbose(!m_Controls->m_InteractiveBox->isChecked()); m_ParentNode = m_InputImageNodes.at(0); m_TrackingThread.start(QThread::LowestPriority); } 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 5e8138d..7acc145 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 @@ -1,1674 +1,1674 @@ QmitkStreamlineTrackingViewControls 0 0 453 859 0 0 QmitkTemplate QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 3 3 0 40 QFrame::NoFrame QFrame::Raised 0 15 0 0 6 15 true 0 0 true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 true Save parameters to json file Save Parameters :/QmitkTractography/download.png:/QmitkTractography/download.png true Load parameters from json file Load Parameters :/QmitkTractography/upload.png:/QmitkTractography/upload.png false Start Tractography :/QmitkTractography/right.png:/QmitkTractography/right.png true Stop tractography and return all fibers reconstructed until now. Stop Tractography :/QmitkTractography/stop.png:/QmitkTractography/stop.png QFrame::NoFrame QFrame::Raised 0 0 0 0 Input Image. ODF, tensor and peak images are currently supported. Input Image: Input Image. ODF, tensor, peak, and, in case of ML tractography, raw diffusion-weighted images are currently supported. <html><head/><body><p><span style=" color:#ff0000;">select image in data-manager</span></p></body></html> true Tractography Forest: 0 0 0 0 true 0 0 0 421 254 Seeding Specify how, where and how many tractography seed points are placed. QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Number of seed points equally distributed around selected position. 1 9999999 50 Radius: Seedpoints are equally distributed within a sphere centered at the selected position with the specified radius (in mm). 2 50.000000000000000 0.100000000000000 2.000000000000000 Num. Seeds: true When checked, parameter changes cause instant retracking while in interactive mode. Update on Parameter Change true QFrame::NoFrame QFrame::Raised 0 0 0 0 Try each seed N times until a valid streamline is obtained (only for probabilistic tractography). Minimum fiber length (in mm) 1 999 10 Trials Per Seed: Max. Num. Fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed (-1 means no limit). -1 999999999 -1 QFrame::NoFrame QFrame::Raised 0 0 0 0 Seeds per Voxel: Seed Image: Number of seed points placed in each voxel. 1 9999999 true Dynamically pick a seed location by click into image. Enable Interactive Tractography Qt::Vertical 20 40 0 0 541 175 ROI Constraints Specify various ROI and mask images to constrain the tractography process. Mask Image: Select which fibers should be accepted or rejected based on the location of their endpoints. No Constraints on EP locations Both EPs in Target Image Both EPs in Target Image But Different Label One EP in Seed Image and One EP in Target Image At Least One EP in Target Image Exactly One EP in Target Image No EP in Target Image Endpoint Constraints: Stop ROI Image: Exclusion ROI Image: Target ROI Image: Qt::Vertical 20 40 0 -270 421 459 Tractography Parameters Specify the behavior of the tractography at each streamline integration step (step size, deterministic/probabilistic, ...). Additional threshold on the ODF magnitude. This is useful in case of CSD fODF tractography. For fODFs a good default value is 0.1, for normalized dODFs, e.g. Q-ball ODFs, this threshold should be very low (0.00025) or 0. 5 1.000000000000000 0.100000000000000 0.000250000000000 Important for probabilistic peak tractography and peak prior. Actual jitter is drawn from a normal distribution with peak_jitter*fabs(direction_value) as standard deviation. 3 1.000000000000000 0.100000000000000 0.010000000000000 Fix Random Seed: Qt::Vertical 20 40 Mode: Cutoff: Minimum tract length in mm. Shorter fibers are discarded. Minimum fiber length (in mm) 1 999.000000000000000 1.000000000000000 20.000000000000000 Angular Threshold: 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 Maximum allowed angular SDTEV over 4 voxel lengths. Default: 30° -1 180 30 g: Always produce the same random numbers. Minimum tract length in mm. Shorter fibers are discarded. Maximum fiber length (in mm) 1 999.000000000000000 1.000000000000000 400.000000000000000 Step size (in voxels) 2 0.010000000000000 10.000000000000000 0.100000000000000 0.500000000000000 Sharpen ODFs: Threshold on peak magnitude, FA, GFA, ... 5 1.000000000000000 0.100000000000000 0.100000000000000 Peak Jitter: Loop Check: Step Size: Max. Tract Length: FA/GFA Image: ODF Cutoff: 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 Angular threshold between two steps (in degree). Default: 90° * step_size -1 90 1 -1 Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. Deterministic Probabilistic 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: Min. Tract Length: Rais ODF to the power of X 1 8 Second Order: - Always produce the same random numbers. + Use second order integration to avoid streamline overshoot true 0 0 435 189 Tractography Prior Weight: Weighting factor between prior and data. 1.000000000000000 0.100000000000000 0.500000000000000 Peak Image: Qt::Vertical 20 40 If unchecked, the prior cannot create directions where there are none in the data. true New Directions from Prior: Restrict to Prior: Restrict tractography to regions where the prior is valid. true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 y x z Flip Directions: 0 0 435 189 Neighborhood Sampling Specify if and how information about the current streamline neighborhood should be used. Only neighborhood samples in front of the current streamline position are considered. Use Only Frontal Samples false If checked, the majority of sampling points has to place a stop-vote for the streamline to terminate. If not checked, all sampling positions have to vote for a streamline termination. Use Stop-Votes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Samples: Number of neighborhood samples that are used to determine the next fiber progression direction. 50 Sampling Distance: Sampling distance (in voxels) 2 10.000000000000000 0.100000000000000 0.250000000000000 Qt::Vertical 20 40 0 0 435 189 Data Handling Specify interpolation and direction flips. QFrame::NoFrame QFrame::Raised 0 0 0 0 Trilinearly interpolate the input image used for tractography. Interpolate Tractography Data true Trilinearly interpolate the ROI images used to constrain the tractography. Interpolate ROI Images true QFrame::NoFrame QFrame::Raised 0 0 0 0 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 Flip directions: Qt::Vertical 20 40 0 0 435 189 Output and Postprocessing Specify the tractography output (streamlines or probability maps) and postprocessing steps. Qt::Vertical 20 40 Compress fibers using the specified error constraint. Compress Fibers true Output map with voxel-wise visitation counts instead of streamlines. Output Probability Map false QmitkSingleNodeSelectionWidget QWidget
QmitkSingleNodeSelectionWidget.h
1