diff --git a/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx b/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx index b6010dd2b6..5f154bc14d 100644 --- a/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx +++ b/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx @@ -1,253 +1,254 @@ /*=================================================================== 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. ===================================================================*/ /*========================================================================= Program: Tensor ToolKit - TTK Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $ Language: C++ Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $ Version: $Revision: 68 $ Copyright (c) INRIA 2010. All rights reserved. See LICENSE.txt for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_ #define _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_ #endif #define _USE_MATH_DEFINES #include "itkElectrostaticRepulsionDiffusionGradientReductionFilter.h" #include #include #include #include namespace itk { template ElectrostaticRepulsionDiffusionGradientReductionFilter ::ElectrostaticRepulsionDiffusionGradientReductionFilter() { this->SetNumberOfRequiredInputs( 1 ); } template double ElectrostaticRepulsionDiffusionGradientReductionFilter ::Costs() { double costs = 2*M_PI; for (IndicesVector::iterator it = m_UsedGradientIndices.begin(); it!=m_UsedGradientIndices.end(); ++it) { for (IndicesVector::iterator it2 = m_UsedGradientIndices.begin(); it2!=m_UsedGradientIndices.end(); ++it2) if (it != it2) { vnl_vector_fixed v1 = m_OriginalGradientDirections->at(*it); vnl_vector_fixed v2 = m_OriginalGradientDirections->at(*it2); v1.normalize(); v2.normalize(); double temp = dot_product(v1,v2); if (temp>1) temp = 1; else if (temp<-1) temp = -1; double angle = acos(temp); if (angle1) temp = 1; else if (temp<-1) temp = -1; angle = acos(temp); if (angle void ElectrostaticRepulsionDiffusionGradientReductionFilter ::GenerateData() { unsigned int randSeed = time(NULL); if(m_InputBValueMap.empty()) { // if no InputMap is set, do the same for each shell m_InputBValueMap = m_OriginalBValueMap; } if(m_InputBValueMap.find(0) != m_InputBValueMap.end()) { //delete b0 from input BValueMap m_InputBValueMap.erase(0); } BValueMap manipulatedMap = m_OriginalBValueMap; int shellCounter = 0; for(BValueMap::iterator it = m_InputBValueMap.begin(); it != m_InputBValueMap.end(); it++ ) { srand(randSeed); // initialize index vectors m_UsedGradientIndices.clear(); m_UnusedGradientIndices.clear(); if ( it->second.size() <= m_NumGradientDirections[shellCounter] ) { itkWarningMacro( << "current directions: " << it->second.size() << " wanted directions: " << m_NumGradientDirections[shellCounter]); m_NumGradientDirections[shellCounter] = it->second.size(); shellCounter++; continue; } MITK_INFO << "Shell number: " << shellCounter; int c=0; for (int i=0; isecond.size(); i++) { if (csecond.at(i)); else m_UnusedGradientIndices.push_back(it->second.at(i)); c++; } double minAngle = Costs(); double newMinAngle = 0; MITK_INFO << "minimum angle: " << 180*minAngle/M_PI; int stagnationCount = 0; int rejectionCount = 0; int maxRejections = 10000;// m_NumGradientDirections[shellCounter] * 1000; int iUsed = 0; - while ( stagnationCount<1000 && rejectionCount minAngle) // accept or reject proposal + if (m_UsedGradientIndices.size()>0) + while ( stagnationCount<1000 && rejectionCount minAngle) // accept or reject proposal + { + MITK_INFO << "minimum angle: " << 180*newMinAngle/M_PI; + + if ( (newMinAngle-minAngle)<0.01 ) + stagnationCount++; + else + stagnationCount = 0; + + minAngle = newMinAngle; + rejectionCount = 0; + } else - stagnationCount = 0; - - minAngle = newMinAngle; - rejectionCount = 0; + { + rejectionCount++; + m_UsedGradientIndices.at(iUsed) = vUsed; + m_UnusedGradientIndices.at(iUnUsed) = vUnUsed; + } + iUsed++; + iUsed = iUsed % m_UsedGradientIndices.size(); } - else - { - rejectionCount++; - m_UsedGradientIndices.at(iUsed) = vUsed; - m_UnusedGradientIndices.at(iUnUsed) = vUnUsed; - } - iUsed++; - iUsed = iUsed % m_UsedGradientIndices.size(); - } manipulatedMap[it->first] = m_UsedGradientIndices; shellCounter++; } int vecLength = 0 ; for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++) vecLength += it->second.size(); // initialize output image typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion()); outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() ); outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() ); outImage->SetVectorLength( vecLength ); // Set the vector length outImage->Allocate(); itk::ImageRegionIterator< OutputImageType > newIt(outImage, outImage->GetLargestPossibleRegion()); newIt.GoToBegin(); typename InputImageType::Pointer inImage = const_cast(this->GetInput(0)); itk::ImageRegionIterator< InputImageType > oldIt(inImage, inImage->GetLargestPossibleRegion()); oldIt.GoToBegin(); // initial new value of voxel OutputPixelType newVec; newVec.SetSize( vecLength ); newVec.AllocateElements( vecLength ); // generate new pixel values while(!newIt.IsAtEnd()) { // init new vector with zeros newVec.Fill(0.0); InputPixelType oldVec = oldIt.Get(); int index = 0; for(BValueMap::iterator it=manipulatedMap.begin(); it!=manipulatedMap.end(); it++) for(int j=0; jsecond.size(); j++) { newVec[index] = oldVec[it->second.at(j)]; index++; } newIt.Set(newVec); ++newIt; ++oldIt; } // set new gradient directions m_GradientDirections = GradientDirectionContainerType::New(); int index = 0; for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++) for(int j = 0; j < it->second.size(); j++) { m_GradientDirections->InsertElement(index, m_OriginalGradientDirections->at(it->second.at(j))); index++; } this->SetNumberOfRequiredOutputs (1); this->SetNthOutput (0, outImage); MITK_INFO << "...done"; } } // end of namespace diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp index 1f2e3b2634..17d080956d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,520 +1,521 @@ /*=================================================================== 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. ===================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkB0ImageExtractionToSeparateImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include // mitk includes #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include #include #include const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_DiffusionImage(NULL) { } QmitkPreprocessingView::QmitkPreprocessingView(const QmitkPreprocessingView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkPreprocessingView::~QmitkPreprocessingView() { } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_MeasurementFrameTable->horizontalHeader()->setResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setResizeMode(QHeaderView::Stretch); } } void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkPreprocessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { + m_Controls->m_ReductionFrame->setLayout(new QGridLayout); connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) ); connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) ); connect( (QObject*)(m_Controls->m_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) ); connect( (QObject*)(m_Controls->m_ModifyMeasurementFrame), SIGNAL(clicked()), this, SLOT(DoApplyMesurementFrame()) ); connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) ); connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) ); connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) ); } } void QmitkPreprocessingView::OnSelectionChanged( std::vector nodes ) { bool foundDwiVolume = false; m_DiffusionImage = NULL; m_SelectedDiffusionNodes.clear(); // iterate selection for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast*>(node->GetData()) ) { foundDwiVolume = true; m_DiffusionImage = dynamic_cast*>(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); m_SelectedDiffusionNodes.push_back(node); } } m_Controls->m_ButtonBrainMask->setEnabled(foundDwiVolume); m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume); m_Controls->m_ModifyMeasurementFrame->setEnabled(foundDwiVolume); m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); foreach(QCheckBox * box, m_ReduceGradientCheckboxes) { m_Controls->m_ReductionFrame->layout()->removeWidget(box); delete box; } foreach(QSpinBox * box, m_ReduceGradientSpinboxes) { m_Controls->m_ReductionFrame->layout()->removeWidget(box); delete box; } m_ReduceGradientCheckboxes.clear(); m_ReduceGradientSpinboxes.clear(); if (foundDwiVolume) { vnl_matrix_fixed< double, 3, 3 > mf = m_DiffusionImage->GetMeasurementFrame(); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(mf.get(r,c))); m_Controls->m_MeasurementFrameTable->setItem(r,c,item); } typedef mitk::DiffusionImage::BValueMap BValueMap; typedef mitk::DiffusionImage::BValueMap::iterator BValueMapIterator; BValueMap bValMap = m_DiffusionImage->GetB_ValueMap(); BValueMapIterator it = bValMap.begin(); m_Controls->m_BvalueTable->clear(); m_Controls->m_BvalueTable->setRowCount(bValMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList); QCheckBox* checkBox; QSpinBox* spinBox; int i = 0 ; for(;it != bValMap.end(); it++) { m_Controls->m_BvalueTable->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); m_Controls->m_BvalueTable->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); // Reduce Gradients GUI adaption if(it->first != 0 && bValMap.size() > 1){ checkBox = new QCheckBox(QString::number(it->first) + " with " + QString::number(it->second.size()) + " directions"); checkBox->setEnabled(true); checkBox->setChecked(true); checkBox->setCheckable(true); m_ReduceGradientCheckboxes.push_back(checkBox); m_Controls->m_ReductionFrame->layout()->addWidget(checkBox); spinBox = new QSpinBox(); spinBox->setValue(std::ceil((float)it->second.size()/2)); spinBox->setMaximum(it->second.size()); spinBox->setMinimum(0); m_ReduceGradientSpinboxes.push_back(spinBox); m_Controls->m_ReductionFrame->layout()->addWidget(spinBox); } i++; } } else { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); delete item; item = new QTableWidgetItem(); m_Controls->m_MeasurementFrameTable->setItem(r,c,item); } m_Controls->m_BvalueTable->clear(); m_Controls->m_BvalueTable->setRowCount(1); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList); m_Controls->m_BvalueTable->setItem(0,0,new QTableWidgetItem("-")); m_Controls->m_BvalueTable->setItem(0,1,new QTableWidgetItem("-")); m_Controls->m_DiffusionImageLabel->setText("-"); } } void QmitkPreprocessingView::Activated() { QmitkFunctionality::Activated(); } void QmitkPreprocessingView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); for (int j=0; jSize(); j++) if (gradientContainer->at(j)[0]<0) gradientContainer->at(j) = -gradientContainer->at(j); m_DiffusionImage->SetDirections(gradientContainer); } void QmitkPreprocessingView::DoApplyMesurementFrame() { if (m_DiffusionImage.IsNull()) return; vnl_matrix_fixed< double, 3, 3 > mf; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); if (!item) return; mf[r][c] = item->text().toDouble(); } m_DiffusionImage->SetMeasurementFrame(mf); } void QmitkPreprocessingView::DoShowGradientDirections() { if (m_DiffusionImage.IsNull()) return; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (int j=0; jSize(); j++) { mitk::Point3D p; vnl_vector_fixed< double, 3 > v = gradientContainer->at(j); if (v.magnitude()>mitk::eps) { p[0] = v[0]*100; p[1] = v[1]*100; p[2] = v[2]*100; pointset->InsertPoint(j, p); } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(pointset); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); name += "_GradientDirections"; node->SetName(name.toStdString().c_str()); node->SetProperty("pointsize", mitk::FloatProperty::New(2.5)); node->SetProperty("color", mitk::ColorProperty::New(1,0,0)); GetDefaultDataStorage()->Add(node); } void QmitkPreprocessingView::DoReduceGradientDirections() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter FilterType; typedef DiffusionImageType::BValueMap BValueMap; // GetShellSelection from GUI BValueMap shellSlectionMap; BValueMap originalShellMap = m_DiffusionImage->GetB_ValueMap(); std::vector newNumGradientDirections; int shellCounter = 0; foreach(QCheckBox * box , m_ReduceGradientCheckboxes) { if(box->isChecked()) { double BValue = (box->text().split(' ')).at(0).toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; newNumGradientDirections.push_back(m_ReduceGradientSpinboxes.at(shellCounter)->value()); } shellCounter++; } GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(newNumGradientDirections); filter->SetOriginalBValueMap(originalShellMap); filter->SetShellSelectionBValueMap(shellSlectionMap); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(m_DiffusionImage->GetB_Value()); image->SetDirections(filter->GetGradientDirections()); image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); foreach(QSpinBox* box, m_ReduceGradientSpinboxes) { name += "_"; name += QString::number(box->value()); } imageNode->SetName(name.toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() { typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; // call the extraction withou averaging if the check-box is checked if( this->m_Controls->m_CheckExtractAll->isChecked() ) { DoExtractBOWithoutAveraging(); return; } mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0")); GetDefaultDataStorage()->Add(node); ++itemiter; } } void QmitkPreprocessingView::DoExtractBOWithoutAveraging() { // typedefs typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType; // check number of selected objects, return if empty int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0_ALL")); GetDefaultDataStorage()->Add(node); ++itemiter; } } void QmitkPreprocessingView::AverageGradients() { int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); vols->AverageRedundantGradients(m_Controls->m_Blur->value()); ++itemiter; } } void QmitkPreprocessingView::BrainMask() { int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); typedef itk::CastImageFilter, itk::Image > CastFilterType; CastFilterType::Pointer castfilter = CastFilterType::New(); castfilter->SetInput(filter->GetOutput()); typedef itk::BrainMaskExtractionImageFilter MaskFilterType; MaskFilterType::Pointer maskfilter = MaskFilterType::New(); maskfilter->SetInput(castfilter->GetOutput()); maskfilter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( maskfilter->GetOutput() ); mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask")); GetDefaultDataStorage()->Add(node); ++itemiter; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui index 0a0a71dcc0..e38818d6bf 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui @@ -1,535 +1,549 @@ QmitkPreprocessingViewControls 0 0 389 989 0 0 false QmitkPreprocessingViewControls true Data Diffusion Image: - 0 0 Info 0 0 Qt::ScrollBarAsNeeded Qt::ScrollBarAlwaysOff true 100 true false true b-Value Number of gradients false Generate pointset displaying the gradient vectors. Show gradients Qt::Horizontal 40 20 Reduce size 0 70 Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them anyway by taking into account all directions within a certain radius. true QFrame::NoFrame QFrame::Raised 0 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. 6 2.000000000000000 0.000100000000000 0.001000000000000 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Merge radius false Average redundant gradients false Mirror all gradients around one axis. Mirror gradients to half sphere Qt::Horizontal + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 9 + + + 9 + + + + + Specify desired number of gradients per shell. + + + + + + + + + + + + + false Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere. Reduce number of gradients - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - - Non diffusion weighted image 0 30 Average and extract all images that were acquired without diffusion weighting. true false Extract B0 Create a 3D+t data set containing all b0 images as timesteps Extract all B0 without averaging Brain mask false Estimate binary brain mask 0 0 Measurment frame Qt::Horizontal 40 20 false 0 0 10 10 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true false true true New Row New Row New Row New Column New Column New Column false Apply new mesurement frame Qt::Vertical 20 40