diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp index d31555e28e..746806fec4 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp @@ -1,2158 +1,2156 @@ /*=================================================================== 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 "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include -#define _USE_MATH_DEFINES -#include - QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ m_View->m_TractsToDwiFilter->Update(); } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImageNode( nullptr ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); // connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; m_TractsToDwiFilter->SetAbortGenerateData(true); m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::Image::Pointer mitkImage = mitk::Image::New(); statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage = mitk::GrabItkImageMemory( m_TractsToDwiFilter->GetOutput() ); mitk::DiffusionPropertyHelper::SetGradientContainer(mitkImage, parameters.m_SignalGen.GetItkGradientContainer()); mitk::DiffusionPropertyHelper::SetReferenceBValue(mitkImage, parameters.m_SignalGen.GetBvalue()); mitk::DiffusionPropertyHelper::InitializeImage( mitkImage ); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); if (m_Controls->m_VolumeFractionsBox->isChecked()) { if (m_TractsToDwiFilter->GetPhaseImage().IsNotNull()) { mitk::Image::Pointer phaseImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = m_TractsToDwiFilter->GetPhaseImage(); phaseImage = mitk::GrabItkImageMemory( itkPhase.GetPointer() ); mitk::DataNode::Pointer phaseNode = mitk::DataNode::New(); phaseNode->SetData( phaseImage ); phaseNode->SetName("Phase Image"); GetDataStorage()->Add(phaseNode, parameters.m_Misc.m_ResultNode); } if (m_TractsToDwiFilter->GetKspaceImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = m_TractsToDwiFilter->GetKspaceImage(); image = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("k-Space"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_TractsToDwiFilter->GetCoilPointset()); node->SetName("Coil Positions"); node->SetProperty("pointsize", mitk::FloatProperty::New(parameters.m_SignalGen.m_ImageSpacing[0]/4)); node->SetProperty("color", mitk::ColorProperty::New(0, 1, 0)); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } int c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = m_TractsToDwiFilter->GetOutputImagesReal(); for (auto real : output_real) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(real.GetPointer()); image->SetVolume(real->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-real"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = m_TractsToDwiFilter->GetOutputImagesImag(); for (auto imag : output_imag) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(imag.GetPointer()); image->SetVolume(imag->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-imag"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } } m_TractsToDwiFilter = nullptr; if (parameters.m_Misc.m_AfterSimulationMessage.size()>0) QMessageBox::information( nullptr, "Warning", parameters.m_Misc.m_AfterSimulationMessage.c_str()); mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_Misc.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); SaveParameters(outputFileName+".ffp"); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::Save(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_SignalGen.m_FrequencyMap = nullptr; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_BallWidget2->SetT1(4658); m_Controls->m_BallWidget2->SetT2(2200); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->SetT1(4658); m_Controls->m_AstrosticksWidget2->SetT2(2200); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_DotWidget2->SetT1(4658); m_Controls->m_DotWidget2->SetT2(2200); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp2FractionFrame->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_ZeroRinging->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_Controls->m_DriftFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp1VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp2VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp3VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TemplateComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_FiberBundleComboBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isFiberBundle = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New( ); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("Odfmage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer isNonDiffMitkImage = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isBinaryMitkImage = mitk::NodePredicateAnd::New( isNonDiffMitkImage, isBinaryPredicate ); m_Controls->m_FrequencyMapBox->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp2VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp2VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp3VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp3VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp4VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp4VolumeFraction->SetZeroEntryText("--"); m_Controls->m_MaskComboBox->SetPredicate(isBinaryMitkImage); m_Controls->m_MaskComboBox->SetZeroEntryText("--"); m_Controls->m_TemplateComboBox->SetPredicate(isMitkImage); m_Controls->m_TemplateComboBox->SetZeroEntryText("--"); m_Controls->m_FiberBundleComboBox->SetPredicate(isFiberBundle); m_Controls->m_FiberBundleComboBox->SetZeroEntryText("--"); QFont font; font.setFamily("Courier"); font.setStyleHint(QFont::Monospace); font.setFixedPitch(true); font.setPointSize(7); m_Controls->m_SimulationStatusText->setFont(font); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_AddDrift, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDrift(int))); connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddRinging(int))); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_UseBvalsBvecsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(OnBvalsBvecsCheck(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); connect((QObject*) m_Controls->m_LoadBvalsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvalsEdit())); connect((QObject*) m_Controls->m_LoadBvecsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvecsEdit())); connect((QObject*) m_Controls->m_MaskComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnMaskSelected(int))); connect((QObject*) m_Controls->m_TemplateComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnTemplateSelected(int))); connect((QObject*) m_Controls->m_FiberBundleComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnFibSelected(int))); connect((QObject*) m_Controls->m_LineReadoutTimeBox, SIGNAL( valueChanged(double)), (QObject*) this, SLOT(OnTlineChanged())); + connect((QObject*) m_Controls->m_SizeX, SIGNAL( valueChanged(int)), (QObject*) this, SLOT(OnTlineChanged())); } OnTlineChanged(); UpdateGui(); } void QmitkFiberfoxView::OnTlineChanged() { - unsigned int num_pix_line = 0; + double num_pix_line = 0; if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); num_pix_line = img->GetDimension(0); } else if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) // use geometry of mask image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); num_pix_line = img->GetDimension(0); } else { - num_pix_line = static_cast(m_Controls->m_SizeX->value()); + num_pix_line = m_Controls->m_SizeX->value(); } - double value = m_Controls->m_LineReadoutTimeBox->value(); -// double dweel_pp = value/num_pix_line; - double bw = 1000.0/value; + double value = static_cast(m_Controls->m_LineReadoutTimeBox->value())/1000.0; // line readout time in seconds + double dweel_pp = value/num_pix_line; // pixel readout time in seconds + double bw = 1/dweel_pp; double bw_pp = bw/num_pix_line; - std::string tt = "Bandwidth:\n" + boost::lexical_cast(static_cast(bw)) + "Hz\n" + boost::lexical_cast(static_cast(bw_pp)) + "Hz/Px"; + std::string tt = "Bandwidth:\n" + boost::lexical_cast(itk::Math::Round(bw)) + "Hz\n" + boost::lexical_cast(itk::Math::Round(bw_pp)) + "Hz/Px"; m_Controls->m_LineReadoutTimeBox->setToolTip(tt.c_str()); } void QmitkFiberfoxView::OnMaskSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnTemplateSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnFibSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnBvalsBvecsCheck(int ) { UpdateGui(); } void QmitkFiberfoxView::UpdateParametersFromGui() { m_Parameters.ClearSignalParameters(); m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked(); m_Parameters.m_Misc.m_CheckOutputVolumeFractionsBox = m_Controls->m_VolumeFractionsBox->isChecked(); std::string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { m_Parameters.m_Misc.m_OutputPath = outputPath; m_Parameters.m_Misc.m_OutputPath += "/"; } else { m_Parameters.m_Misc.m_OutputPath = ""; } if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); mitk::CastToItkImage(mitkMaskImage, m_Parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); m_Parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) // use parameters of selected DWI { mitk::Image::Pointer dwi = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(dwi, itkVectorImagePointer); m_Parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); m_Parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi)); m_Parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(dwi)); } else if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) // use geometry of mask image { ItkUcharImgType::Pointer itkImg = m_Parameters.m_SignalGen.m_MaskImage; m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else // use GUI parameters { m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); m_Parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); m_Parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); m_Parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); m_Parameters.m_SignalGen.m_ImageOrigin[0] = m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_Parameters.m_SignalGen.m_ImageOrigin[1] = m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_Parameters.m_SignalGen.m_ImageOrigin[2] = m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_Parameters.m_SignalGen.m_ImageDirection.SetIdentity(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } // signal relaxation m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; if (m_Controls->m_RelaxationBox->isChecked()) { m_Parameters.m_SignalGen.m_DoSimulateRelaxation = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RELAX"; } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = m_Parameters.m_SignalGen.m_DoSimulateRelaxation; // N/2 ghosts m_Parameters.m_Misc.m_DoAddGhosts = m_Controls->m_AddGhosts->isChecked(); m_Parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); if (m_Controls->m_AddGhosts->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_GHOST"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_Parameters.m_SignalGen.m_KspaceLineOffset)); } // Aliasing m_Parameters.m_Misc.m_DoAddAliasing = m_Controls->m_AddAliasing->isChecked(); m_Parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; if (m_Controls->m_AddAliasing->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes m_Parameters.m_Misc.m_DoAddSpikes = m_Controls->m_AddSpikes->isChecked(); m_Parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); m_Parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); if (m_Controls->m_AddSpikes->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_Parameters.m_SignalGen.m_Spikes)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_Parameters.m_SignalGen.m_SpikeAmplitude)); } // Drift m_Parameters.m_SignalGen.m_DoAddDrift = m_Controls->m_AddDrift->isChecked(); m_Parameters.m_SignalGen.m_Drift = static_cast(m_Controls->m_DriftFactor->value())/100; if (m_Controls->m_AddDrift->isChecked()) { m_Parameters.m_Misc.m_ArtifactModelString += "_DRIFT"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Drift", FloatProperty::New(m_Parameters.m_SignalGen.m_Drift)); } // gibbs ringing m_Parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); m_Parameters.m_SignalGen.m_ZeroRinging = m_Controls->m_ZeroRinging->value(); if (m_Controls->m_AddGibbsRinging->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions m_Parameters.m_Misc.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkFloatImgType::Pointer itkImg = ItkFloatImgType::New(); CastToItkImage< ItkFloatImgType >(img, itkImg); if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map { m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); m_Parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } m_Parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); m_Parameters.m_Misc.m_DoAddEddyCurrents = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_EDDY"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_Parameters.m_SignalGen.m_EddyStrength)); } // Motion m_Parameters.m_SignalGen.m_DoAddMotion = false; m_Parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); m_Parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); m_Parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); m_Parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); m_Parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); m_Parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); m_Parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); m_Parameters.m_SignalGen.m_MotionVolumes.clear(); m_Parameters.m_Misc.m_MotionVolumesBox = m_Controls->m_MotionVolumesBox->text().toStdString(); if ( m_Controls->m_AddMotion->isChecked()) { m_Parameters.m_SignalGen.m_DoAddMotion = true; m_Parameters.m_Misc.m_ArtifactModelString += "_MOTION"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_Parameters.m_SignalGen.m_DoRandomizeMotion)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[2])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[2])); if ( m_Parameters.m_Misc.m_MotionVolumesBox == "random" ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Parameters.m_Misc.m_MotionVolumesBox.empty() ) { std::stringstream stream( m_Parameters.m_Misc.m_MotionVolumesBox ); std::vector numbers; int number = std::numeric_limits::max(); while( stream >> number ) { if( number < std::numeric_limits::max() ) { numbers.push_back( number ); } } // If a list of negative numbers is given: if( *(std::min_element( numbers.begin(), numbers.end() )) < 0 && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( true ); } // set all true except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( -(*iter) < (int)m_Parameters.m_SignalGen.GetNumVolumes() && -(*iter) >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( -(*iter) ) = false; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of negative numbers."; } // If a list of positive numbers is given: else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0 && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( false ); } // set all false except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( *iter < (int)m_Parameters.m_SignalGen.GetNumVolumes() && *iter >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( *iter ) = true; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of positive numbers."; } else { MITK_ERROR << "QmitkFiberfoxView.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; } } else { m_Parameters.m_Misc.m_MotionVolumesBox = ""; // set empty. m_Controls->m_MotionVolumesBox->setText(""); for (unsigned int i=0; im_AcquisitionTypeBox->currentIndex(); m_Parameters.m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)m_Controls->m_CoilSensBox->currentIndex(); m_Parameters.m_SignalGen.m_NumberOfCoils = m_Controls->m_NumCoilsBox->value(); m_Parameters.m_SignalGen.m_PartialFourier = m_Controls->m_PartialFourier->value(); m_Parameters.m_SignalGen.m_ReversePhase = m_Controls->m_ReversePhaseBox->isChecked(); m_Parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); m_Parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); m_Parameters.m_SignalGen.m_EchoTrainLength = m_Controls->m_EtlBox->value(); m_Parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); m_Parameters.m_SignalGen.m_tRep = m_Controls->m_TRbox->value(); m_Parameters.m_SignalGen.m_tInv = m_Controls->m_TIbox->value(); m_Parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); m_Parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); m_Parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); // double voxelVolume = m_Parameters.m_SignalGen.m_ImageSpacing[0] // * m_Parameters.m_SignalGen.m_ImageSpacing[1] // * m_Parameters.m_SignalGen.m_ImageSpacing[2]; // if ( m_Parameters.m_SignalGen.m_SignalScale*voxelVolume > itk::NumericTraits::max()*0.75 ) // { // m_Parameters.m_SignalGen.m_SignalScale = itk::NumericTraits::max()*0.75/voxelVolume; // m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); // QMessageBox::information( nullptr, "Warning", // "Maximum signal exceeding data type limits. Automatically adjusted to " // + QString::number(m_Parameters.m_SignalGen.m_SignalScale) // + " to obtain a maximum signal of 75% of the data type maximum." // " Relaxation and other effects that affect the signal intensities are not accounted for."); // } // Noise m_Parameters.m_Misc.m_DoAddNoise = m_Controls->m_AddNoise->isChecked(); m_Parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value(); if (m_Controls->m_AddNoise->isChecked()) { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } case 1: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } case 2: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } default: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } } if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_Misc.m_ArtifactModelString += QString::number(m_Parameters.m_SignalGen.m_NoiseVariance).toStdString(); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(m_Parameters.m_SignalGen.m_NoiseVariance)); } } // signal models { // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); model->SetT2(m_Controls->m_StickWidget1->GetT2()); model->SetT1(m_Controls->m_StickWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); model->SetT2(m_Controls->m_TensorWidget1->GetT2()); model->SetT1(m_Controls->m_TensorWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp1VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp1VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget2->GetD()); model->SetT2(m_Controls->m_StickWidget2->GetT2()); model->SetT1(m_Controls->m_StickWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); model->SetT2(m_Controls->m_TensorWidget2->GetT2()); model->SetT1(m_Controls->m_TensorWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } } if (m_Controls->m_Comp2VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_FiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp2VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget1->GetD()); model->SetT2(m_Controls->m_BallWidget1->GetT2()); model->SetT1(m_Controls->m_BallWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget1->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; } case 2: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget1->GetT2()); model->SetT1(m_Controls->m_DotWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp3VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp3VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget2->GetD()); model->SetT2(m_Controls->m_BallWidget2->GetT2()); model->SetT1(m_Controls->m_BallWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget2->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; } case 3: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget2->GetT2()); model->SetT1(m_Controls->m_DotWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 4: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp4VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_NonFiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer compVolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, compVolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(compVolumeImage); } } m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Parameters.m_SignalGen.m_SignalScale)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Parameters.m_SignalGen.m_AxonRadius)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_Parameters.m_SignalGen.m_tInhom)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.echoTrainLength", IntProperty::New(m_Parameters.m_SignalGen.m_EchoTrainLength)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_Parameters.m_SignalGen.m_tLine)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_Parameters.m_SignalGen.m_tEcho)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_Parameters.m_SignalGen.GetBvalue())); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_Parameters.m_SignalGen.m_DoDisablePartialVolume)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_Parameters.m_SignalGen.m_DoSimulateRelaxation)); m_Parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); } void QmitkFiberfoxView::SaveParameters(QString filename) { UpdateParametersFromGui(); std::vector< int > bVals = m_Parameters.m_SignalGen.GetBvalues(); std::cout << "b-values: "; for (auto v : bVals) std::cout << v << " "; std::cout << std::endl; bool ok = true; bool first = true; bool dosampling = false; mitk::Image::Pointer diffImg = nullptr; itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); } else { model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); } if ( model!=nullptr && model->GetNumberOfKernels() <= 0 ) { if (first==true) { if ( QMessageBox::question(nullptr, "Prototype signal sampling", "Do you want to sample prototype signals from the selected diffusion-weighted imag and save them?", QMessageBox::Yes, QMessageBox::No) == QMessageBox::Yes ) dosampling = true; first = false; if ( dosampling && (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull() || !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) ) { QMessageBox::information(nullptr, "Parameter file not saved", "No diffusion-weighted image selected to sample signal from."); return; } else if (dosampling) { diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } } typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); if (dosampling && diffImg.IsNotNull()) { ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) { QMessageBox::information( nullptr, "Parameter file not saved", "No valid prototype signals could be sampled."); return; } } } } m_Parameters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberfoxView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); SaveParameters(filename); } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; m_Parameters.LoadParameters(filename.toStdString()); if (m_Parameters.m_MissingTags.size()>0) { QString missing("Parameter file might be corrupted. The following parameters could not be read: "); missing += QString(m_Parameters.m_MissingTags.c_str()); missing += "\nDefault values have been assigned to the missing parameters."; QMessageBox::information( nullptr, "Warning!", missing); } // image generation parameters m_Controls->m_SizeX->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[2]); m_Controls->m_NumGradientsBox->setValue(m_Parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(m_Parameters.m_SignalGen.GetBvalue()); m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(m_Parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(m_Parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(m_Parameters.m_SignalGen.m_tInhom); m_Controls->m_EtlBox->setValue(m_Parameters.m_SignalGen.m_EchoTrainLength); m_Controls->m_FiberRadius->setValue(m_Parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(m_Parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(m_Parameters.m_SignalGen.m_DoDisablePartialVolume); m_Controls->m_ReversePhaseBox->setChecked(m_Parameters.m_SignalGen.m_ReversePhase); m_Controls->m_PartialFourier->setValue(m_Parameters.m_SignalGen.m_PartialFourier); m_Controls->m_TRbox->setValue(m_Parameters.m_SignalGen.m_tRep); m_Controls->m_TIbox->setValue(m_Parameters.m_SignalGen.m_tInv); m_Controls->m_NumCoilsBox->setValue(m_Parameters.m_SignalGen.m_NumberOfCoils); m_Controls->m_CoilSensBox->setCurrentIndex(m_Parameters.m_SignalGen.m_CoilSensitivityProfile); m_Controls->m_AcquisitionTypeBox->setCurrentIndex(m_Parameters.m_SignalGen.m_AcquisitionType); if (!m_Parameters.m_Misc.m_BvalsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvalsEdit->setText(QString(m_Parameters.m_Misc.m_BvalsFile.c_str())); } else m_Controls->m_LoadBvalsEdit->setText("-"); if (!m_Parameters.m_Misc.m_BvecsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvecsEdit->setText(QString(m_Parameters.m_Misc.m_BvecsFile.c_str())); } else m_Controls->m_LoadBvecsEdit->setText("-"); if (m_Parameters.m_NoiseModel!=nullptr) { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); } else if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); } m_Controls->m_NoiseLevel->setValue(m_Parameters.m_NoiseModel->GetNoiseVariance()); } else { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); m_Controls->m_NoiseLevel->setValue(m_Parameters.m_SignalGen.m_NoiseVariance); } m_Controls->m_VolumeFractionsBox->setChecked(m_Parameters.m_Misc.m_CheckOutputVolumeFractionsBox); m_Controls->m_AdvancedOptionsBox_2->setChecked(m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox); m_Controls->m_AddGhosts->setChecked(m_Parameters.m_Misc.m_DoAddGhosts); m_Controls->m_AddAliasing->setChecked(m_Parameters.m_Misc.m_DoAddAliasing); m_Controls->m_AddDistortions->setChecked(m_Parameters.m_Misc.m_DoAddDistortions); m_Controls->m_AddSpikes->setChecked(m_Parameters.m_Misc.m_DoAddSpikes); m_Controls->m_AddEddy->setChecked(m_Parameters.m_Misc.m_DoAddEddyCurrents); m_Controls->m_AddDrift->setChecked(m_Parameters.m_SignalGen.m_DoAddDrift); m_Controls->m_kOffsetBox->setValue(m_Parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_WrapBox->setValue(100*(1-m_Parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_DriftFactor->setValue(100*m_Parameters.m_SignalGen.m_Drift); m_Controls->m_SpikeNumBox->setValue(m_Parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(m_Parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_EddyGradientStrength->setValue(m_Parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(m_Parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_ZeroRinging->setValue(m_Parameters.m_SignalGen.m_ZeroRinging); m_Controls->m_AddMotion->setChecked(m_Parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(m_Parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MotionVolumesBox->setText(QString(m_Parameters.m_Misc.m_MotionVolumesBox.c_str())); m_Controls->m_MaxTranslationBoxX->setValue(m_Parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(m_Parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(m_Parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(m_Parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(m_Parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(m_Parameters.m_SignalGen.m_Rotation[2]); m_Controls->m_Compartment1Box->setCurrentIndex(0); m_Controls->m_Compartment2Box->setCurrentIndex(0); m_Controls->m_Compartment3Box->setCurrentIndex(0); m_Controls->m_Compartment4Box->setCurrentIndex(0); for (unsigned int i=0; i* signalModel = nullptr; if (iGetVolumeFractionImage().IsNotNull() ) { compVolNode = mitk::DataNode::New(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(signalModel->GetVolumeFractionImage().GetPointer()); image->SetVolume(signalModel->GetVolumeFractionImage()->GetBufferPointer()); compVolNode->SetData( image ); compVolNode->SetName("Compartment volume "+QString::number(signalModel->m_CompartmentId).toStdString()); GetDataStorage()->Add(compVolNode); } switch (signalModel->m_CompartmentId) { case 1: { if (compVolNode.IsNotNull()) m_Controls->m_Comp1VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget1->SetT2(model->GetT2()); m_Controls->m_StickWidget1->SetT1(model->GetT1()); m_Controls->m_StickWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment1Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget1->SetT2(model->GetT2()); m_Controls->m_TensorWidget1->SetT1(model->GetT1()); m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment1Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment1Box->setCurrentIndex(3); break; } break; } case 2: { if (compVolNode.IsNotNull()) m_Controls->m_Comp2VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget2->SetT2(model->GetT2()); m_Controls->m_StickWidget2->SetT1(model->GetT1()); m_Controls->m_StickWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment2Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget2->SetT2(model->GetT2()); m_Controls->m_TensorWidget2->SetT1(model->GetT1()); m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment2Box->setCurrentIndex(3); break; } break; } case 3: { if (compVolNode.IsNotNull()) m_Controls->m_Comp3VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget1->SetT2(model->GetT2()); m_Controls->m_BallWidget1->SetT1(model->GetT1()); m_Controls->m_BallWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment3Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget1->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment3Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget1->SetT2(model->GetT2()); m_Controls->m_DotWidget1->SetT1(model->GetT1()); m_Controls->m_Compartment3Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment3Box->setCurrentIndex(3); break; } break; } case 4: { if (compVolNode.IsNotNull()) m_Controls->m_Comp4VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget2->SetT2(model->GetT2()); m_Controls->m_BallWidget2->SetT1(model->GetT1()); m_Controls->m_BallWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment4Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget2->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment4Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget2->SetT2(model->GetT2()); m_Controls->m_DotWidget2->SetT1(model->GetT1()); m_Controls->m_Compartment4Box->setCurrentIndex(3); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment4Box->setCurrentIndex(4); break; } break; } } } if ( m_Parameters.m_SignalGen.m_MaskImage ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_MaskImage.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_MaskImage->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Tissue mask"); GetDataStorage()->Add(node); m_Controls->m_MaskComboBox->SetSelectedNode(node); } if ( m_Parameters.m_SignalGen.m_FrequencyMap ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_FrequencyMap.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_FrequencyMap->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Frequency map"); GetDataStorage()->Add(node); m_Controls->m_FrequencyMapBox->SetSelectedNode(node); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_Comp2FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDrift(int value) { if (value>0) m_Controls->m_DriftFrame->setVisible(true); else m_Controls->m_DriftFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnAddRinging(int value) { if (value>0) m_Controls->m_ZeroRinging->setVisible(true); else m_Controls->m_ZeroRinging->setVisible(false); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*itk::Math::pi); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::GenerateImage() { if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNull() && !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Point3D origin; origin[0] = m_Controls->m_SpacingX->value()/2; origin[1] = m_Controls->m_SpacingY->value()/2; origin[2] = m_Controls->m_SpacingZ->value()/2; image->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); GetDataStorage()->Add(node); m_SelectedImageNode = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); QMessageBox::information(nullptr, "Template image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image. A template image with the specified geometry has been generated that can be used to draw artificial fibers (see view 'Fiber Generator')."); } else if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull()) SimulateImageFromFibers(m_Controls->m_FiberBundleComboBox->GetSelectedNode()); else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode()) ) SimulateForExistingDwi(m_Controls->m_TemplateComboBox->GetSelectedNode()); else QMessageBox::information(nullptr, "No image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image."); } void QmitkFiberfoxView::SetFocus() { } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(imageNode->GetData())) ); if ( !isDiffusionImage ) { return; } UpdateParametersFromGui(); mitk::Image::Pointer diffImg = dynamic_cast(imageNode->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = imageNode; m_Parameters.m_SignalGen.m_SignalScale = 1; m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetInputImage(itkVectorImagePointer); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundle::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) { return; } UpdateParametersFromGui(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = fiberNode; m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast (m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { bool first = true; bool ok = true; mitk::Image::Pointer diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); if (model!=0 && model->GetNumberOfKernels()<=0) { if (first==true) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) break; } } if (!ok) { QMessageBox::information( nullptr, "Simulation cancelled", "No valid prototype signals could be sampled."); return; } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( nullptr, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SetBvalsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvals file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvalsEdit->setText("-"); else m_Controls->m_LoadBvalsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetBvecsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvecs file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvecsEdit->setText("-"); else m_Controls->m_LoadBvecsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG std::string outputPath; outputPath = QFileDialog::getExistingDirectory(nullptr, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } } void QmitkFiberfoxView::UpdateGui() { OnTlineChanged(); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) m_Controls->m_LoadGradientsFrame->setVisible(true); else m_Controls->m_GenerateGradientsFrame->setVisible(true); // Signal generation gui if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull() || m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); } } 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 21bffa95fa..c59bf0cffa 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 @@ -1,2891 +1,2891 @@ QmitkFiberfoxViewControls 0 0 490 2775 Form QGroupBox { background-color: transparent; } Intra-axonal Compartment 6 6 6 6 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. QGroupBox { background-color: transparent; } Inter-axonal Compartment 6 6 6 6 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. QGroupBox { background-color: transparent; } Image Settings 6 6 6 6 color: rgb(255, 0, 0); Using geometry of selected image! QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Inversion time (in ms) for inversion recovery sequences. If 0, no inversion pulse is simulated. 0 999999999 1 0 <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 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 TE in milliseconds 1 999999999 1 100 Partial Fourier: false Partial fourier factor (0.5-1) 3 0.500000000000000 1.000000000000000 0.100000000000000 1.000000000000000 Output one image per compartment containing the corresponding volume fractions per voxel. Reverse Phase Encoding Direction false Dwell time (time to read one line in k-space) in ms. 4 100.000000000000000 0.100000000000000 - 0.020000000000000 + 1.000000000000000 Number of coil elements used for the acquisiton. 1 128 1 1 Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 9999.000000000000000 Dwell Time: false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Acquisition Type: Fiber Radius: Signal Scale: <html><head/><body><p>Number of Channels:</p></body></html> false TR in milliseconds 1 999999999 1 4000 Single Shot EPI Conventional Spin Echo Fast Spin Echo 1 100000 1 100 Constant Linear Exponential <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 <html><head/><body><p>Coil Sensitivity:</p></body></html> false <html><head/><body><p>Inversion Time <span style=" font-style:italic;">TI</span>: </p></body></html> false Output phase image and volume fraction maps. Output Additional Images false <html><head/><body><p>Echo Train Length: </p></body></html> false Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse) 1 999999999 1 8 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <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 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 Advanced Options color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 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 Use bvals/bvecs files QFrame::NoFrame QFrame::Raised 0 0 0 0 ... ... - false Bvecs: false Bvals: false - false QGroupBox { background-color: transparent; } Extra-axonal Compartments 6 6 6 6 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 QGroupBox { background-color: transparent; } Noise and other Artifacts 6 6 6 6 Qt::Horizontal true QFrame::NoFrame QFrame::Raised 0 6 0 0 6 Toggle between random movement and linear movement. Randomize motion true QGroupBox { background-color: transparent; } Rotation 6 9 6 6 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 QGroupBox { background-color: transparent; } Translation 6 6 6 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 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 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 40.000000000000000 Qt::Horizontal true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Signal Reduction (%): false Global signal in last simulated volume is specified percentage lower than in the first volume. 1 100.000000000000000 1.000000000000000 6.000000000000000 true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Gradient: false Eddy current induced magnetic field gradient (in mT/m). 5 1000.000000000000000 0.001000000000000 0.002000000000000 Qt::Horizontal Add Eddy Current Effects false Add Distortions false Add Spikes false Add Signal Drift false 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 Qt::Horizontal 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 Motion Artifacts false Add N/2 Ghosts false Qt::Horizontal Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Qt::Horizontal Add Noise false Qt::Horizontal Add Aliasing false If > 0, ringing is simulated by by setting the defined percentage of higher frequencies to 0 in k-space. Otherwise, the input to the k-space simulation is generated with twice the resolution and cropped during k-space simulation (much slower). 100 10 Qt::Vertical 20 40 QFrame::NoFrame QFrame::Raised 0 0 0 0 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> Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico 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> Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 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 QGroupBox { background-color: transparent; } Input Data 6 6 6 6 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 true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Courier 7 true QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.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 m_FiberBundleComboBox m_MaskComboBox m_TemplateComboBox m_SavePathEdit m_OutputPathButton m_GenerateImageButton m_AbortSimulationButton m_SimulationStatusText m_LoadParametersButton m_SaveParametersButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_UseBvalsBvecsBox m_LoadBvalsEdit m_LoadBvalsButton m_LoadBvecsEdit m_LoadBvecsButton m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_AcquisitionTypeBox m_SignalScaleBox m_NumCoilsBox m_CoilSensBox m_TEbox m_TRbox m_TIbox 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_AddDrift m_DriftFactor m_AddMotion m_RandomMotion m_MotionVolumesBox m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_ZeroRinging