void StartSimulation(FiberfoxParameters<double> parameters, FiberBundle::Pointer fiberBundle, mitk::Image::Pointer refImage, string message)
{
itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
tractsToDwiFilter->SetUseConstantRandSeed(true);
tractsToDwiFilter->SetParameters(parameters);
tractsToDwiFilter->SetFiberBundle(fiberBundle);
tractsToDwiFilter->Update();
mitk::Image::Pointer testImage = mitk::GrabItkImageMemory( tractsToDwiFilter->GetOutput() );
testImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( parameters.m_SignalGen.GetGradientDirections() ) );
testImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( parameters.m_SignalGen.m_Bvalue ) );
mitk::DiffusionPropertyHelper propertyHelper( testImage );
propertyHelper.InitializeImage();
if (refImage.IsNotNull())
{
if( static_cast<mitk::GradientDirectionsProperty*>( refImage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer().IsNotNull() )
{
ItkDwiType::Pointer itkTestImagePointer = ItkDwiType::New();
mitk::CastToItkImage(testImage, itkTestImagePointer);
ItkDwiType::Pointer itkRefImagePointer = ItkDwiType::New();
mitk::CastToItkImage(refImage, itkRefImagePointer);
bool cond = CompareDwi(itkTestImagePointer, itkRefImagePointer);
if (!cond)
{
MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath();
mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi");
mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi");
}
MITK_TEST_CONDITION_REQUIRED(cond, message);
}
}
}
mitk::Image::Pointer ResampleDWIbySpacing(mitk::Image::Pointer input, float* spacing, bool useLinInt = true)
{
itk::Vector<double, 3> spacingVector;
spacingVector[0] = spacing[0];
spacingVector[1] = spacing[1];
spacingVector[2] = spacing[2];
typedef itk::ResampleDwiImageFilter<short> ResampleFilterType;
mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
mitk::CastToItkImage(input, itkVectorImagePointer);
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInput( itkVectorImagePointer );
resampler->SetInterpolation(ResampleFilterType::Interpolate_Linear);
resampler->SetNewSpacing(spacingVector);
resampler->Update();
mitk::Image::Pointer output = mitk::GrabItkImageMemory( resampler->GetOutput() );
output->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( mitk::DiffusionPropertyHelper::GetGradientContainer(input) ) );
output->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( mitk::DiffusionPropertyHelper::GetReferenceBValue(input) ) );
mitk::DiffusionPropertyHelper propertyHelper( output );
propertyHelper.InitializeImage();
return output;
}
bool mitk::DiffusionDICOMFileReader
::LoadSingleOutputImage( DiffusionHeaderDICOMFileReader::DICOMHeaderListType retrievedHeader,
DICOMImageBlockDescriptor& block, bool is_mosaic)
{
// prepare data reading
DiffusionDICOMFileReaderHelper helper;
DiffusionDICOMFileReaderHelper::VolumeFileNamesContainer filenames;
const DICOMImageFrameList& frames = block.GetImageFrameList();
int numberOfDWImages = block.GetIntProperty("timesteps", 1);
int numberOfFramesPerDWImage = frames.size() / numberOfDWImages;
assert( int( double((double) frames.size() / (double) numberOfDWImages)) == numberOfFramesPerDWImage );
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
std::vector< std::string > FileNamesPerVolume;
auto timeStepStart = frames.begin() + idx * numberOfFramesPerDWImage;
auto timeStepEnd = frames.begin() + (idx+1) * numberOfFramesPerDWImage;
for (auto frameIter = timeStepStart;
frameIter != timeStepEnd;
++frameIter)
{
FileNamesPerVolume.push_back( (*frameIter)->Filename );
}
filenames.push_back( FileNamesPerVolume );
}
// TODO : only prototyping to test loading of diffusion images
// we need some solution for the different types
mitk::Image::Pointer output_image = mitk::Image::New();
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer directions =
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New();
double max_bvalue = 0;
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
if( max_bvalue < header.b_value )
max_bvalue = header.b_value;
}
// normalize the retrieved gradient directions according to the set b-value (maximal one)
for( int idx = 0; idx < numberOfDWImages; idx++ )
{
DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
mitk::DiffusionPropertyHelper::GradientDirectionType grad = header.g_vector;
grad.normalize();
grad *= sqrt( header.b_value / max_bvalue );
directions->push_back( grad );
}
// initialize the output image
output_image->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( directions ) );
output_image->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( max_bvalue ) );
if( is_mosaic && this->m_ResolveMosaic )
{
mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::Pointer mosaic_reader =
mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::New();
// retrieve the remaining meta-information needed for mosaic reconstruction
// it suffices to get it exemplatory from the first file in the file list
mosaic_reader->RetrieveMosaicInformation( filenames.at(0).at(0) );
mitk::MosaicDescriptor mdesc = mosaic_reader->GetMosaicDescriptor();
mitk::CastToMitkImage( helper.LoadMosaicToVector<short, 3>( filenames, mdesc ), output_image );
}
else
{
mitk::CastToMitkImage( helper.LoadToVector<short, 3>( filenames ), output_image );
}
mitk::DiffusionPropertyHelper propertyHelper( output_image );
propertyHelper.InitializeImage();
output_image->SetProperty("diffusion.dicom.importname", mitk::StringProperty::New( helper.GetOutputName(filenames) ) );
block.SetMitkImage( (mitk::Image::Pointer) output_image );
return block.GetMitkImage().IsNotNull();
}
/*!
\brief Fits the tractogram to the input peak image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092).
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Fit Fibers To Image");
parser.setCategory("Fiber Tracking and Processing Methods");
parser.setDescription("Assigns a weight to each fiber in order to optimally explain the input peak image");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (.fib, vtk ascii file format)", us::Any(), false);
parser.addArgument("", "i2", mitkCommandLineParser::InputFile, "Input image:", "input image", us::Any(), false);
parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false);
parser.addArgument("max_iter", "", mitkCommandLineParser::Int, "Max. iterations:", "maximum number of optimizer iterations", 20);
parser.addArgument("bundle_based", "", mitkCommandLineParser::Bool, "Bundle based fit:", "fit one weight per input tractogram/bundle, not for each fiber", false);
parser.addArgument("min_g", "", mitkCommandLineParser::Float, "Min. g:", "lower termination threshold for gradient magnitude", 1e-5);
parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 0.1);
parser.addArgument("save_res", "", mitkCommandLineParser::Bool, "Save Residuals:", "save residual images", false);
parser.addArgument("save_weights", "", mitkCommandLineParser::Bool, "Save Weights:", "save fiber weights in a separate text file", false);
parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false);
parser.addArgument("join_tracts", "", mitkCommandLineParser::Bool, "Join output tracts:", "outout tracts are merged into a single tractogram", false);
parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM, Variance, VoxelVariance (default), Lasso, GroupLasso, GroupVariance, NONE");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
mitkCommandLineParser::StringContainerType fib_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i1"]);
std::string input_image_name = us::any_cast<std::string>(parsedArgs["i2"]);
std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
bool single_fib = true;
if (parsedArgs.count("bundle_based"))
single_fib = !us::any_cast<bool>(parsedArgs["bundle_based"]);
bool save_residuals = false;
if (parsedArgs.count("save_res"))
save_residuals = us::any_cast<bool>(parsedArgs["save_res"]);
bool save_weights = false;
if (parsedArgs.count("save_weights"))
save_weights = us::any_cast<bool>(parsedArgs["save_weights"]);
std::string regu = "VoxelVariance";
if (parsedArgs.count("regu"))
regu = us::any_cast<std::string>(parsedArgs["regu"]);
bool join_tracts = false;
if (parsedArgs.count("join_tracts"))
join_tracts = us::any_cast<bool>(parsedArgs["join_tracts"]);
int max_iter = 20;
if (parsedArgs.count("max_iter"))
max_iter = us::any_cast<int>(parsedArgs["max_iter"]);
float g_tol = 1e-5;
if (parsedArgs.count("min_g"))
g_tol = us::any_cast<float>(parsedArgs["min_g"]);
float lambda = 0.1;
if (parsedArgs.count("lambda"))
lambda = us::any_cast<float>(parsedArgs["lambda"]);
bool filter_outliers = false;
if (parsedArgs.count("filter_outliers"))
filter_outliers = us::any_cast<bool>(parsedArgs["filter_outliers"]);
try
{
MITK_INFO << "Loading data";
std::streambuf *old = cout.rdbuf(); // <-- save
std::stringstream ss;
std::cout.rdbuf (ss.rdbuf()); // <-- redirect
std::vector< mitk::FiberBundle::Pointer > input_tracts;
mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {});
std::vector< std::string > fib_names;
for (auto item : fib_files)
{
if ( ist::FileIsDirectory(item) )
{
for ( auto fibFile : get_file_list(item) )
{
mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(fibFile);
if (inputTractogram.IsNull())
continue;
input_tracts.push_back(inputTractogram);
fib_names.push_back(fibFile);
}
}
else
{
mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(item);
if (inputTractogram.IsNull())
continue;
input_tracts.push_back(inputTractogram);
fib_names.push_back(item);
}
}
std::cout.rdbuf (old); // <-- restore
itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input_image_name, &functor)[0].GetPointer();
mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(inputData.GetPointer());
mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast<mitk::PeakImage*>(inputData.GetPointer());
if (mitk_peak_image.IsNotNull())
{
typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitk_peak_image);
caster->Update();
mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
fitter->SetPeakImage(peak_image);
}
else if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
{
fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image));
mitk::TensorModel<>* model = new mitk::TensorModel<>();
model->SetBvalue(1000);
model->SetDiffusivity1(0.0010);
model->SetDiffusivity2(0.00015);
model->SetDiffusivity3(0.00015);
model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image));
fitter->SetSignalModel(model);
}
else if (mitk_image->GetDimension()==3)
{
itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New();
mitk::CastToItkImage(mitk_image, scalar_image);
fitter->SetScalarImage(scalar_image);
}
else
{
MITK_INFO << "Input image invalid. Valid options are peak image, 3D scalar image or raw diffusion-weighted image.";
return EXIT_FAILURE;
}
fitter->SetTractograms(input_tracts);
fitter->SetFitIndividualFibers(single_fib);
fitter->SetMaxIterations(max_iter);
fitter->SetGradientTolerance(g_tol);
fitter->SetLambda(lambda);
fitter->SetFilterOutliers(filter_outliers);
if (regu=="MSM")
fitter->SetRegularization(VnlCostFunction::REGU::MSM);
else if (regu=="Variance")
fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE);
else if (regu=="Lasso")
fitter->SetRegularization(VnlCostFunction::REGU::LASSO);
else if (regu=="VoxelVariance")
fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE);
else if (regu=="GroupLasso")
fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO);
else if (regu=="GroupVariance")
fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE);
else if (regu=="NONE")
fitter->SetRegularization(VnlCostFunction::REGU::NONE);
fitter->Update();
if (save_residuals && mitk_peak_image.IsNotNull())
{
itk::ImageFileWriter< PeakImgType >::Pointer writer = itk::ImageFileWriter< PeakImgType >::New();
writer->SetInput(fitter->GetFittedImage());
writer->SetFileName(outRoot + "_fitted.nii.gz");
writer->Update();
writer->SetInput(fitter->GetResidualImage());
writer->SetFileName(outRoot + "_residual.nii.gz");
writer->Update();
writer->SetInput(fitter->GetOverexplainedImage());
writer->SetFileName(outRoot + "_overexplained.nii.gz");
writer->Update();
writer->SetInput(fitter->GetUnderexplainedImage());
writer->SetFileName(outRoot + "_underexplained.nii.gz");
writer->Update();
}
else if (save_residuals && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
{
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_fitted_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_residual_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetOverexplainedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_overexplained_image.nii.gz");
}
{
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetUnderexplainedImageDiff().GetPointer() );
mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_underexplained_image.nii.gz");
}
}
else if (save_residuals)
{
itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::Pointer writer = itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::New();
writer->SetInput(fitter->GetFittedImageScalar());
writer->SetFileName(outRoot + "_fitted_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetResidualImageScalar());
writer->SetFileName(outRoot + "_residual_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetOverexplainedImageScalar());
writer->SetFileName(outRoot + "_overexplained_image.nii.gz");
writer->Update();
writer->SetInput(fitter->GetUnderexplainedImageScalar());
writer->SetFileName(outRoot + "_underexplained_image.nii.gz");
writer->Update();
}
std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
if (!join_tracts)
{
for (unsigned int bundle=0; bundle<output_tracts.size(); bundle++)
{
std::string name = fib_names.at(bundle);
name = ist::GetFilenameWithoutExtension(name);
mitk::IOUtil::Save(output_tracts.at(bundle), outRoot + name + "_fitted.fib");
if (save_weights)
{
ofstream logfile;
logfile.open (outRoot + name + "_weights.txt");
for (int f=0; f<output_tracts.at(bundle)->GetNumFibers(); ++f)
logfile << output_tracts.at(bundle)->GetFiberWeight(f) << "\n";
logfile.close();
}
}
}
else
{
mitk::FiberBundle::Pointer out = mitk::FiberBundle::New();
out = out->AddBundles(output_tracts);
out->ColorFibersByFiberWeights(false, true);
mitk::IOUtil::Save(out, outRoot + "_fitted.fib");
if (save_weights)
{
ofstream logfile;
logfile.open (outRoot + "_weights.txt");
for (int f=0; f<out->GetNumFibers(); ++f)
logfile << out->GetFiberWeight(f) << "\n";
logfile.close();
}
}
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
int mitkExtractSingleShellTest( int argc, char* argv[] )
{
MITK_TEST_BEGIN("mitkExtractSingleShellTest");
MITK_TEST_CONDITION_REQUIRED( argc > 3, "Specify input and output and the shell to be extracted");
/*
1. Get input data
*/
mitk::Image::Pointer dwimage = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load( argv[1] )[0].GetPointer());
mitk::GradientDirectionsProperty::Pointer gradientsProperty = static_cast<mitk::GradientDirectionsProperty *>( dwimage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() );
MITK_TEST_CONDITION_REQUIRED( gradientsProperty.IsNotNull(), "Input is a dw-image");
unsigned int extract_value = 0;
std::istringstream input(argv[3]);
input >> extract_value;
typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMap;
// GetShellSelection from GUI
BValueMap shellSelectionMap;
BValueMap originalShellMap = static_cast<mitk::BValueMapProperty*>(dwimage->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() )->GetBValueMap();
std::vector<unsigned int> newNumGradientDirections;
shellSelectionMap[extract_value] = originalShellMap[extract_value];
newNumGradientDirections.push_back( originalShellMap[extract_value].size() ) ;
itk::VectorImage< short, 3 >::Pointer itkVectorImagePointer = itk::VectorImage< short, 3 >::New();
mitk::CastToItkImage(dwimage, itkVectorImagePointer);
itk::VectorImage< short, 3 > *vectorImage = itkVectorImagePointer.GetPointer();
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainer = static_cast<mitk::GradientDirectionsProperty*>( dwimage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer();
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vectorImage);
filter->SetOriginalGradientDirections(gradientContainer);
filter->SetNumGradientDirections(newNumGradientDirections);
filter->SetOriginalBValueMap(originalShellMap);
filter->SetShellSelectionBValueMap(shellSelectionMap);
try
{
filter->Update();
}
catch( const itk::ExceptionObject& e)
{
MITK_TEST_FAILED_MSG( << "Failed due to ITK exception: " << e.what() );
}
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
mitk::DiffusionPropertyHelper::CopyProperties(dwimage, outImage, true);
outImage->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( filter->GetGradientDirections() ) );
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
/*
* 3. Write output data
**/
try
{
mitk::IOUtil::Save(outImage, argv[2]);
}
catch( const itk::ExceptionObject& e)
{
MITK_ERROR << "Catched exception: " << e.what();
mitkThrow() << "Failed with exception from subprocess!";
}
MITK_TEST_END();
}
