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 mitk::DWIHeadMotionCorrectionFilter<DiffusionPixelType>
::GenerateData()
{
typedef itk::SplitDWImageFilter< DiffusionPixelType, DiffusionPixelType> SplitFilterType;
DiffusionImageType* input = const_cast<DiffusionImageType*>(this->GetInput(0));
unsigned int numberOfSteps = input->GetVectorImage()->GetNumberOfComponentsPerPixel () ;
m_Steps = numberOfSteps;
//
// (1) Extract the b-zero images to a 3d+t image, register them by NCorr metric and
// rigid registration : they will then be used are reference image for registering
// the gradient images
//
typedef itk::B0ImageExtractionToSeparateImageFilter< DiffusionPixelType, DiffusionPixelType> B0ExtractorType;
typename B0ExtractorType::Pointer b0_extractor = B0ExtractorType::New();
b0_extractor->SetInput( input->GetVectorImage() );
b0_extractor->SetDirections( input->GetDirections() );
b0_extractor->Update();
mitk::Image::Pointer b0Image = mitk::Image::New();
b0Image->InitializeByItk( b0_extractor->GetOutput() );
b0Image->SetImportChannel( b0_extractor->GetOutput()->GetBufferPointer(),
mitk::Image::CopyMemory );
// (2.1) Use the extractor to access the extracted b0 volumes
mitk::ImageTimeSelector::Pointer t_selector =
mitk::ImageTimeSelector::New();
t_selector->SetInput( b0Image );
t_selector->SetTimeNr(0);
t_selector->Update();
// first unweighted image as reference space for the registration
mitk::Image::Pointer b0referenceImage = t_selector->GetOutput();
mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New();
registrationMethod->SetFixedImage( b0referenceImage );
registrationMethod->SetTransformToRigid();
// the unweighted images are of same modality
registrationMethod->SetCrossModalityOff();
// use the advanced (windowed sinc) interpolation
registrationMethod->SetUseAdvancedInterpolation(true);
// Initialize the temporary output image
mitk::Image::Pointer registeredB0Image = b0Image->Clone();
const unsigned int numberOfb0Images = b0Image->GetTimeSteps();
if( numberOfb0Images > 1)
{
mitk::ImageTimeSelector::Pointer t_selector2 =
mitk::ImageTimeSelector::New();
t_selector2->SetInput( b0Image );
for( unsigned int i=1; i<numberOfb0Images; i++)
{
m_CurrentStep = i + 1;
if( m_AbortRegistration == true) {
m_IsInValidState = false;
mitkThrow() << "Stopped by user.";
};
t_selector2->SetTimeNr(i);
t_selector2->Update();
registrationMethod->SetMovingImage( t_selector2->GetOutput() );
try
{
MITK_INFO << " === (" << i <<"/"<< numberOfb0Images-1 << ") :: Starting registration";
registrationMethod->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
mitkThrow() << "Failed to register the b0 images, the PyramidRegistration threw an exception: \n" << e.what();
}
// import volume to the inter-results
mitk::ImageWriteAccessor imac(registrationMethod->GetResampledMovingImage());
registeredB0Image->SetImportVolume( imac.GetData(),
i, 0, mitk::Image::ReferenceMemory );
}
// use the accumulateImageFilter as provided by the ItkAccumulateFilter method in the header file
AccessFixedDimensionByItk_1(registeredB0Image, ItkAccumulateFilter, (4), b0referenceImage );
}
//
// (2) Split the diffusion image into a 3d+t regular image, extract only the weighted images
//
typename SplitFilterType::Pointer split_filter = SplitFilterType::New();
split_filter->SetInput (input->GetVectorImage() );
split_filter->SetExtractAllAboveThreshold(20, input->GetB_ValueMap() );
try
{
split_filter->Update();
}
catch( const itk::ExceptionObject &e)
{
m_IsInValidState = false;
mitkThrow() << " Caught exception from SplitImageFilter : " << e.what();
}
mitk::Image::Pointer splittedImage = mitk::Image::New();
splittedImage->InitializeByItk( split_filter->GetOutput() );
splittedImage->SetImportChannel( split_filter->GetOutput()->GetBufferPointer(),
mitk::Image::CopyMemory );
//
// (3) Use again the time-selector to access the components separately in order
// to perform the registration of Image -> unweighted reference
//
mitk::PyramidImageRegistrationMethod::Pointer weightedRegistrationMethod
= mitk::PyramidImageRegistrationMethod::New();
weightedRegistrationMethod->SetTransformToAffine();
weightedRegistrationMethod->SetCrossModalityOn();
//
// - (3.1) Set the reference image
// - a single b0 image
// - average over the registered b0 images if multiple present
//
weightedRegistrationMethod->SetFixedImage( b0referenceImage );
// use the advanced (windowed sinc) interpolation
weightedRegistrationMethod->SetUseAdvancedInterpolation(true);
//
// - (3.2) Register all timesteps in the splitted image onto the first reference
//
unsigned int maxImageIdx = splittedImage->GetTimeSteps();
mitk::TimeGeometry* tsg = splittedImage->GetTimeGeometry();
mitk::ProportionalTimeGeometry* ptg = dynamic_cast<ProportionalTimeGeometry*>(tsg);
ptg->Expand(maxImageIdx+1);
ptg->SetTimeStepGeometry( ptg->GetGeometryForTimeStep(0), maxImageIdx );
mitk::Image::Pointer registeredWeighted = mitk::Image::New();
registeredWeighted->Initialize( splittedImage->GetPixelType(0), *tsg );
// insert the first unweighted reference as the first volume
mitk::ImageWriteAccessor imac(b0referenceImage);
registeredWeighted->SetImportVolume( imac.GetData(),
0,0, mitk::Image::CopyMemory );
// mitk::Image::Pointer registeredWeighted = splittedImage->Clone();
// this time start at 0, we have only gradient images in the 3d+t file
// the reference image comes form an other image
mitk::ImageTimeSelector::Pointer t_selector_w =
mitk::ImageTimeSelector::New();
t_selector_w->SetInput( splittedImage );
// store the rotation parts of the transformations in a vector
typedef mitk::PyramidImageRegistrationMethod::TransformMatrixType MatrixType;
std::vector< MatrixType > estimated_transforms;
for( unsigned int i=0; i<maxImageIdx; i++)
{
m_CurrentStep = numberOfb0Images + i + 1;
if( m_AbortRegistration == true) {
m_IsInValidState = false;
mitkThrow() << "Stopped by user.";
};
t_selector_w->SetTimeNr(i);
t_selector_w->Update();
weightedRegistrationMethod->SetMovingImage( t_selector_w->GetOutput() );
try
{
MITK_INFO << " === (" << i+1 <<"/"<< maxImageIdx << ") :: Starting registration";
weightedRegistrationMethod->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
mitkThrow() << "Failed to register the b0 images, the PyramidRegistration threw an exception: \n" << e.what();
}
// allow expansion
mitk::ImageWriteAccessor imac(weightedRegistrationMethod->GetResampledMovingImage());
registeredWeighted->SetImportVolume( imac.GetData(),
i+1, 0, mitk::Image::CopyMemory);
estimated_transforms.push_back( weightedRegistrationMethod->GetLastRotationMatrix() );
}
//
// (4) Cast the resulting image back to an diffusion weighted image
//
typename DiffusionImageType::GradientDirectionContainerType *gradients = input->GetDirections();
typename DiffusionImageType::GradientDirectionContainerType::Pointer gradients_new =
DiffusionImageType::GradientDirectionContainerType::New();
typename DiffusionImageType::GradientDirectionType bzero_vector;
bzero_vector.fill(0);
// compose the direction vector
// - no direction for the first image
// - correct ordering of the directions based on the index list
gradients_new->push_back( bzero_vector );
typename SplitFilterType::IndexListType index_list = split_filter->GetIndexList();
typename SplitFilterType::IndexListType::const_iterator lIter = index_list.begin();
while( lIter != index_list.end() )
{
gradients_new->push_back( gradients->at( *lIter ) );
++lIter;
}
typename mitk::ImageToDiffusionImageSource< DiffusionPixelType >::Pointer caster =
mitk::ImageToDiffusionImageSource< DiffusionPixelType >::New();
caster->SetImage( registeredWeighted );
caster->SetBValue( input->GetB_Value() );
caster->SetGradientDirections( gradients_new.GetPointer() );
try
{
caster->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
MITK_ERROR << "Casting back to diffusion image failed: ";
mitkThrow() << "Subprocess failed with exception: " << e.what();
}
//
// (5) Adapt the gradient directions according to the estimated transforms
//
typedef mitk::DiffusionImageCorrectionFilter< DiffusionPixelType > CorrectionFilterType;
typename CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
OutputImagePointerType output = caster->GetOutput();
corrector->SetImage( output );
corrector->CorrectDirections( estimated_transforms );
//
// (6) Pass the corrected image to the filters output port
//
m_CurrentStep += 1;
this->GetOutput()->SetVectorImage(output->GetVectorImage());
this->GetOutput()->SetB_Value(output->GetB_Value());
this->GetOutput()->SetDirections(output->GetDirections());
this->GetOutput()->SetMeasurementFrame(output->GetMeasurementFrame());
this->GetOutput()->InitializeFromVectorImage();
this->GetOutput()->Modified();
}