int GibbsTracking(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("parameters", "p", ctkCommandLineParser::String, "parameter file (.gtp)", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::String, "binary mask image"); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "sh coefficient convention (FSL, MRtrix)", string("FSL"), true); parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", 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 paramFileName = us::any_cast<string>(parsedArgs["parameters"]); string outFileName = us::any_cast<string>(parsedArgs["outFile"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); // instantiate gibbs tracker typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType; typedef itk::Image<OdfVectorType,3> ItkQballImageType; typedef itk::GibbsTrackingFilter<ItkQballImageType> GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); // try to cast to qball image if( boost::algorithm::ends_with(inFileName, ".qbi") ) { MITK_INFO << "Loading qball image ..."; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage<ItkQballImageType>(mitkQballImage, itk_qbi); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { MITK_INFO << "Loading tensor image ..."; 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); gibbsTracker->SetTensorImage(itk_dti); } else if ( boost::algorithm::ends_with(inFileName, ".nii") ) { MITK_INFO << "Loading sh-coefficient image ..."; mitk::Image::Pointer mitkImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer()); int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; int c=3, d=2-2*nrCoeffs; double D = c*c-4*d; int shOrder; if (D>0) { shOrder = (-c+sqrt(D))/2.0; if (shOrder<0) shOrder = (-c-sqrt(D))/2.0; } else if (D==0) shOrder = -c/2.0; MITK_INFO << "using SH-order " << shOrder; int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast<string>(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 1; MITK_INFO << "Using MRtrix style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; switch (shOrder) { case 4: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention)); break; case 6: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention)); break; case 8: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention)); break; case 10: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention)); break; case 12: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention)); break; default: MITK_INFO << "SH-order " << shOrder << " not supported"; } } else return EXIT_FAILURE; // global tracking if (parsedArgs.count("mask")) { typedef itk::Image<float,3> MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage<MaskImgType>(mitkMaskImage, itk_mask); gibbsTracker->SetMaskImage(itk_mask); } gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetLoadParameterFile( paramFileName ); // gibbsTracker->SetLutPath( "" ); gibbsTracker->Update(); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) { (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( mitkFiberBundle.GetPointer() ); } } } 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; }
/**Documentation * Test for gibbs tracking filter */ int mitkGibbsTrackingTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkGibbsTrackingTest"); MITK_TEST_CONDITION_REQUIRED(argc>4,"check for input data") QBallImage::Pointer mitkQballImage; Image::Pointer mitkMaskImage; mitk::FiberBundleX::Pointer fib1; try{ MITK_INFO << "Q-Ball image: " << argv[1]; MITK_INFO << "Mask image: " << argv[2]; MITK_INFO << "Parameter file: " << argv[3]; MITK_INFO << "Reference bundle: " << argv[4]; RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); const std::string s1="", s2=""; std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false ); mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer()); MITK_TEST_CONDITION_REQUIRED(mitkQballImage.IsNotNull(),"check qball image") infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[2], s1, s2, false ); mitkMaskImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer()); MITK_TEST_CONDITION_REQUIRED(mitkMaskImage.IsNotNull(),"check mask image") infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[4], s1, s2, false ); fib1 = dynamic_cast<mitk::FiberBundleX*>(infile.at(0).GetPointer()); MITK_TEST_CONDITION_REQUIRED(fib1.IsNotNull(),"check fiber bundle") typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType; typedef itk::Image<OdfVectorType,3> OdfVectorImgType; typedef itk::Image<float,3> MaskImgType; typedef itk::GibbsTrackingFilter<OdfVectorImgType> GibbsTrackingFilterType; OdfVectorImgType::Pointer itk_qbi = OdfVectorImgType::New(); mitk::CastToItkImage<OdfVectorImgType>(mitkQballImage, itk_qbi); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage<MaskImgType>(mitkMaskImage, itk_mask); GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); gibbsTracker->SetMaskImage(itk_mask); gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetRandomSeed(1); gibbsTracker->SetLoadParameterFile(argv[3]); gibbsTracker->Update(); mitk::FiberBundleX::Pointer fib2 = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "check if gibbs tracking has changed"); gibbsTracker->SetRandomSeed(0); gibbsTracker->Update(); fib2 = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); MITK_TEST_CONDITION_REQUIRED(!fib1->Equals(fib2), "check if gibbs tracking has changed after wrong seed"); } catch(...) { return EXIT_FAILURE; } // always end with this! MITK_TEST_END(); }
int main(int argc, char* argv[]) { std::cout << "GibbsTracking"; mitkCommandLineParser parser; parser.setTitle("Gibbs Tracking"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); parser.addArgument("parameters", "p", mitkCommandLineParser::InputFile, "Parameters:", "parameter file (.gtp)", us::Any(), false); parser.addArgument("mask", "m", mitkCommandLineParser::InputFile, "Mask:", "binary mask image"); parser.addArgument("shConvention", "s", mitkCommandLineParser::String, "SH coefficient:", "sh coefficient convention (FSL, MRtrix)", string("FSL"), true); parser.addArgument("outFile", "o", mitkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false); parser.addArgument("noFlip", "f", mitkCommandLineParser::Bool, "No flip:", "do not flip input image to match MITK coordinate convention"); 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 paramFileName = us::any_cast<string>(parsedArgs["parameters"]); string outFileName = us::any_cast<string>(parsedArgs["outFile"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast<bool>(parsedArgs["noFlip"]); try { // instantiate gibbs tracker typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType; typedef itk::Image<OdfVectorType,3> ItkQballImageType; typedef itk::GibbsTrackingFilter<ItkQballImageType> GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); mitk::Image::Pointer mitkImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer()); // try to cast to qball image if( boost::algorithm::ends_with(inFileName, ".qbi") ) { std::cout << "Loading qball image ..."; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { std::cout << "Loading tensor image ..."; 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(mitkTensorImage, itk_dti); gibbsTracker->SetTensorImage(itk_dti); } else if ( boost::algorithm::ends_with(inFileName, ".nii") ) { std::cout << "Loading sh-coefficient image ..."; int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; int c=3, d=2-2*nrCoeffs; double D = c*c-4*d; int shOrder; if (D>0) { shOrder = (-c+sqrt(D))/2.0; if (shOrder<0) shOrder = (-c-sqrt(D))/2.0; } else if (D==0) shOrder = -c/2.0; std::cout << "using SH-order " << shOrder; int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast<string>(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 1; std::cout << "Using MRtrix style sh-coefficient convention"; } else std::cout << "Using FSL style sh-coefficient convention"; } else std::cout << "Using FSL style sh-coefficient convention"; switch (shOrder) { case 4: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention, noFlip)); break; case 6: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention, noFlip)); break; case 8: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention, noFlip)); break; case 10: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention, noFlip)); break; case 12: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention, noFlip)); break; default: std::cout << "SH-order " << shOrder << " not supported"; } } else return EXIT_FAILURE; // global tracking if (parsedArgs.count("mask")) { typedef itk::Image<float,3> MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage(mitkMaskImage, itk_mask); gibbsTracker->SetMaskImage(itk_mask); } gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetLoadParameterFile( paramFileName ); // gibbsTracker->SetLutPath( "" ); gibbsTracker->Update(); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); mitkFiberBundle->SetReferenceGeometry(mitkImage->GetGeometry()); mitk::IOUtil::SaveBaseData(mitkFiberBundle.GetPointer(), outFileName ); } 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; }