void QmitkTensorReconstructionView::TensorReconstructionWithCorr
(mitk::DataStorage::SetOfObjects::Pointer inImages)
{
try
{
itk::TimeProbe clock;
int nrFiles = inImages->size();
if (!nrFiles) return;
QString status;
mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
typedef mitk::DiffusionImage<DiffusionPixelType> DiffusionImageType;
DiffusionImageType* vols = static_cast<DiffusionImageType*>((*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
++itemiter;
// TENSOR RECONSTRUCTION
clock.Start();
MITK_INFO << "Tensor reconstruction with correction for negative eigenvalues";
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Tensor reconstruction for %s", nodename.c_str()).toAscii());
typedef itk::TensorReconstructionWithEigenvalueCorrectionFilter< DiffusionPixelType, TTensorPixelType > ReconstructionFilter;
float b0Threshold = m_Controls->m_TensorReconstructionThreshold->value();
ReconstructionFilter::Pointer reconFilter = ReconstructionFilter::New();
reconFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() );
reconFilter->SetBValue(vols->GetB_Value());
reconFilter->SetB0Threshold(b0Threshold);
reconFilter->Update();
typedef itk::Image<itk::DiffusionTensor3D<TTensorPixelType>, 3> TensorImageType;
TensorImageType::Pointer outputTensorImg = reconFilter->GetOutput();
typedef itk::ImageRegionIterator<TensorImageType> TensorImageIteratorType;
TensorImageIteratorType tensorIt(outputTensorImg, outputTensorImg->GetRequestedRegion());
tensorIt.GoToBegin();
int negatives = 0;
while(!tensorIt.IsAtEnd())
{
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
TensorType tensor = tensorIt.Get();
TensorType::EigenValuesArrayType ev;
tensor.ComputeEigenValues(ev);
for(unsigned int i=0; i<ev.Size(); i++)
{
if(ev[i] < 0.0)
{
tensor.Fill(0.0);
tensorIt.Set(tensor);
negatives++;
break;
}
}
++tensorIt;
}
MITK_INFO << negatives << " tensors with negative eigenvalues" << std::endl;
mitk::TensorImage::Pointer image = mitk::TensorImage::New();
image->InitializeByItk( outputTensorImg.GetPointer() );
image->SetVolume( outputTensorImg->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( image );
QString newname;
newname = newname.append(nodename.c_str());
newname = newname.append("_dti_corrected");
SetDefaultNodeProperties(node, newname.toStdString());
nodes.push_back(node);
// Corrected diffusion image
// typedef itk::VectorImage<short, 3> ImageType;
// ImageType::Pointer correctedVols = reconFilter->GetVectorImage();
// DiffusionImageType::Pointer correctedDiffusion = DiffusionImageType::New();
// correctedDiffusion->SetVectorImage(correctedVols);
// correctedDiffusion->SetDirections(vols->GetDirections());
// correctedDiffusion->SetB_Value(vols->GetB_Value());
// correctedDiffusion->InitializeFromVectorImage();
// mitk::DataNode::Pointer diffNode = mitk::DataNode::New();
// diffNode->SetData( correctedDiffusion );
// QString diffname;
// diffname = diffname.append(nodename.c_str());
// diffname = diffname.append("corrDiff");
// SetDefaultNodeProperties(diffNode, diffname.toStdString());
// nodes.push_back(diffNode);
mitk::ProgressBar::GetInstance()->Progress();
}
std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
GetDefaultDataStorage()->Add(*nodeIt);
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii());
m_MultiWidget->RequestUpdate();
}
catch (itk::ExceptionObject &ex)
{
MITK_INFO << ex ;
QMessageBox::information(0, "Reconstruction not possible:", ex.GetDescription());
}
}
void QmitkTensorReconstructionView::ItkTensorReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages)
{
try
{
itk::TimeProbe clock;
int nrFiles = inImages->size();
if (!nrFiles) return;
QString status;
mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
mitk::DiffusionImage<DiffusionPixelType>* vols =
static_cast<mitk::DiffusionImage<DiffusionPixelType>*>(
(*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
++itemiter;
// TENSOR RECONSTRUCTION
clock.Start();
MITK_DEBUG << "Tensor reconstruction ";
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Tensor reconstruction for %s", nodename.c_str()).toAscii());
typedef itk::DiffusionTensor3DReconstructionImageFilter<
DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter =
TensorReconstructionImageFilterType::New();
tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() );
tensorReconstructionFilter->SetBValue(vols->GetB_Value());
tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreshold->value() );
tensorReconstructionFilter->Update();
clock.Stop();
MITK_DEBUG << "took " << clock.GetMeanTime() << "s.";
// TENSORS TO DATATREE
mitk::TensorImage::Pointer image = mitk::TensorImage::New();
typedef itk::Image<itk::DiffusionTensor3D<TTensorPixelType>, 3> TensorImageType;
TensorImageType::Pointer tensorImage;
tensorImage = tensorReconstructionFilter->GetOutput();
// Check the tensor for negative eigenvalues
if(m_Controls->m_CheckNegativeEigenvalues->isChecked())
{
typedef itk::ImageRegionIterator<TensorImageType> TensorImageIteratorType;
TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetRequestedRegion());
tensorIt.GoToBegin();
while(!tensorIt.IsAtEnd())
{
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
//typedef itk::Tensor<TTensorPixelType, 3> TensorType2;
TensorType tensor = tensorIt.Get();
TensorType::EigenValuesArrayType ev;
tensor.ComputeEigenValues(ev);
for(unsigned int i=0; i<ev.Size(); i++)
{
if(ev[i] < 0.0)
{
tensor.Fill(0.0);
tensorIt.Set(tensor);
break;
}
}
++tensorIt;
}
}
tensorImage->SetDirection( vols->GetVectorImage()->GetDirection() );
image->InitializeByItk( tensorImage.GetPointer() );
image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( image );
QString newname;
newname = newname.append(nodename.c_str());
newname = newname.append("_dti");
SetDefaultNodeProperties(node, newname.toStdString());
nodes.push_back(node);
mitk::ProgressBar::GetInstance()->Progress();
}
std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
GetDefaultDataStorage()->Add(*nodeIt);
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii());
m_MultiWidget->RequestUpdate();
}
catch (itk::ExceptionObject &ex)
{
MITK_INFO << ex ;
QMessageBox::information(0, "Reconstruction not possible:", ex.GetDescription());
return;
}
}
void QmitkDiffusionQuantificationView::TensorQuantification(
mitk::DataStorage::SetOfObjects::Pointer inImages, int method)
{
itk::TimeProbe clock;
QString status;
int nrFiles = inImages->size();
if (!nrFiles) return;
mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
typedef float TTensorPixelType;
typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType;
typedef itk::Image< TensorPixelType, 3 > TensorImageType;
mitk::Image* vol =
static_cast<mitk::Image*>((*itemiter)->GetData());
TensorImageType::Pointer itkvol = TensorImageType::New();
mitk::CastToItkImage<TensorImageType>(vol, itkvol);
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
++itemiter;
// COMPUTE FA
clock.Start();
MBI_INFO << "Computing FA ";
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
"Computing FA for %s", nodename.c_str()).toAscii());
typedef itk::Image< TTensorPixelType, 3 > FAImageType;
typedef itk::ShiftScaleImageFilter<FAImageType, FAImageType>
ShiftScaleFilterType;
ShiftScaleFilterType::Pointer multi =
ShiftScaleFilterType::New();
multi->SetShift(0.0);
multi->SetScale(m_Controls->m_ScaleImageValuesBox->value());//itk::NumericTraits<RealValueType>::max()
typedef itk::TensorDerivedMeasurementsFilter<TTensorPixelType> MeasurementsType;
if(method == 0) //FA
{
/* typedef itk::TensorFractionalAnisotropyImageFilter<
TensorImageType, FAImageType > FilterType;
FilterType::Pointer anisotropyFilter = FilterType::New();
anisotropyFilter->SetInput( itkvol.GetPointer() );
anisotropyFilter->Update();
multi->SetInput(anisotropyFilter->GetOutput());
nodename = QString(nodename.c_str()).append("_FA").toStdString();*/
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::FA);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_FA").toStdString();
}
else if(method == 1) //RA
{
/*typedef itk::TensorRelativeAnisotropyImageFilter<
TensorImageType, FAImageType > FilterType;
FilterType::Pointer anisotropyFilter = FilterType::New();
anisotropyFilter->SetInput( itkvol.GetPointer() );
anisotropyFilter->Update();
multi->SetInput(anisotropyFilter->GetOutput());
nodename = QString(nodename.c_str()).append("_RA").toStdString();*/
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::RA);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_RA").toStdString();
}
else if(method == 2) // AD (Axial diffusivity)
{
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::AD);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_AD").toStdString();
}
else if(method == 3) // RD (Radial diffusivity, (Lambda2+Lambda3)/2
{
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::RD);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_RD").toStdString();
}
else if(method == 4) // 1-(Lambda2+Lambda3)/(2*Lambda1)
{
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::CA);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_CA").toStdString();
}
else if(method == 5) // MD (Mean Diffusivity, (Lambda1+Lambda2+Lambda3)/3 )
{
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itkvol.GetPointer() );
measurementsCalculator->SetMeasure(MeasurementsType::MD);
measurementsCalculator->Update();
multi->SetInput(measurementsCalculator->GetOutput());
nodename = QString(nodename.c_str()).append("_MD").toStdString();
}
multi->Update();
clock.Stop();
MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
// FA TO DATATREE
mitk::Image::Pointer image = mitk::Image::New();
image->InitializeByItk( multi->GetOutput() );
image->SetVolume( multi->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( image );
node->SetProperty( "name", mitk::StringProperty::New(nodename) );
nodes.push_back(node);
mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
}
std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
GetDefaultDataStorage()->Add(*nodeIt);
m_MultiWidget->RequestUpdate();
}