/**
* Calculate indices derived from Qball or tensor images
*/
int DiffusionIndices(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false);
parser.addArgument("index", "idx", ctkCommandLineParser::String, "index (fa, gfa, ra, ad, rd, ca, l2, l3, md)", us::Any(), false);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output file", us::Any(), false);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
string inFileName = us::any_cast<string>(parsedArgs["input"]);
string index = us::any_cast<string>(parsedArgs["index"]);
string outFileName = us::any_cast<string>(parsedArgs["outFile"]);
string ext = itksys::SystemTools::GetFilenameLastExtension(outFileName);
if (ext.empty())
outFileName += ".nrrd";
try
{
// load input image
const std::string s1="", s2="";
std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false );
if( boost::algorithm::ends_with(inFileName, ".qbi") && index=="gfa" )
{
typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType;
typedef itk::Image<OdfVectorType,3> ItkQballImageType;
mitk::QBallImage::Pointer mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer());
ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New();
mitk::CastToItkImage<ItkQballImageType>(mitkQballImage, itk_qbi);
typedef itk::DiffusionQballGeneralizedFaImageFilter<float,float,QBALL_ODFSIZE> GfaFilterType;
GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
gfaFilter->SetInput(itk_qbi);
gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
gfaFilter->Update();
MITK_INFO << "Writing " << outFileName;
itk::ImageFileWriter< itk::Image<float,3> >::Pointer fileWriter = itk::ImageFileWriter< itk::Image<float,3> >::New();
fileWriter->SetInput(gfaFilter->GetOutput());
fileWriter->SetFileName(outFileName);
fileWriter->Update();
}
else if( boost::algorithm::ends_with(inFileName, ".dti") )
{
typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(infile.at(0).GetPointer());
ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
mitk::CastToItkImage<ItkTensorImage>(mitkTensorImage, itk_dti);
typedef itk::TensorDerivedMeasurementsFilter<float> MeasurementsType;
MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
measurementsCalculator->SetInput(itk_dti.GetPointer() );
if(index=="fa")
measurementsCalculator->SetMeasure(MeasurementsType::FA);
else if(index=="ra")
measurementsCalculator->SetMeasure(MeasurementsType::RA);
else if(index=="ad")
measurementsCalculator->SetMeasure(MeasurementsType::AD);
else if(index=="rd")
measurementsCalculator->SetMeasure(MeasurementsType::RD);
else if(index=="ca")
measurementsCalculator->SetMeasure(MeasurementsType::CA);
else if(index=="l2")
measurementsCalculator->SetMeasure(MeasurementsType::L2);
else if(index=="l3")
measurementsCalculator->SetMeasure(MeasurementsType::L3);
else if(index=="md")
measurementsCalculator->SetMeasure(MeasurementsType::MD);
else
{
MITK_WARN << "No valid diffusion index for input image (tensor image) defined";
return EXIT_FAILURE;
}
measurementsCalculator->Update();
MITK_INFO << "Writing " << outFileName;
itk::ImageFileWriter< itk::Image<float,3> >::Pointer fileWriter = itk::ImageFileWriter< itk::Image<float,3> >::New();
fileWriter->SetInput(measurementsCalculator->GetOutput());
fileWriter->SetFileName(outFileName);
fileWriter->Update();
}
else
MITK_INFO << "Diffusion index " << index << " not supported for supplied file type.";
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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();
}