MINC/SoftwareDevelopment/EZMINC/ITK Integration

Better MINC1/2 support for ITK If you are not satisfied with MINC2 only interface provided by ITK, or need access to MINC file attributes, or want to read/write 4D data use ITK interface provided by EZMINC Installing Compile EZMINC with ITK support, see [EZMINC_Installing] If you are not using ITK plugin (currently plugin is not recommended) add following code to "mincify" your ITK program: #include "itkMincImageIOFactory.h" #include "itkMincImageIO.h" //.... int main(int argc,char **argv) { //registering the MINC_IO factory itk::ObjectFactoryBase::RegisterFactory(itk::MincImageIOFactory::New()); //.... Example of working with DTI data Code from itk_dti.cpp from examples: itk::ImageFileReader<ImageType >::New(); reader->SetFileName(input_file); reader->Update(); ImageType::Pointer img=reader->GetOutput(); double_vector bvalues,direction_x,direction_y,direction_z; //making sure that all vcrtors contain the same number of parameters (just in case) if(!itk::ExposeMetaData<double_vector>( img->GetMetaDataDictionary() , "acquisition:bvalues",bvalues) !itk::ExposeMetaData<double_vector>( img->GetMetaDataDictionary() , "acquisition:direction_x",direction_x) !itk::ExposeMetaData<double_vector>( img->GetMetaDataDictionary() , "acquisition:direction_y",direction_y) direction_x.size() direction_y.size() direction_z.size() ) { std::cerr<<"Different number of components of gradients"<<std::endl; return 2; } std::cout<<"Found "<<bvalues.size()<<" gradient directions"<<std::endl; Using minc XFM files applying transformation code from itk_resample.cpp #include "itkMincImageIOFactory.h" #include "itkMincImageIO.h" #include "minc_helpers.h" typedef itk::ResampleImageFilter<minc::image3d, minc::image3d> FilterType; typedef minc::XfmTransform TransformType; //... TransformType::Pointer transform = TransformType::New(); //reading a minc style xfm file transform->OpenXfm(xfm_f.c_str()); transform->Invert(); filter->SetTransform( transform ); //... Storing affine transformation in .xfm file #include <minc_helpers.h> //... itk::AffineTransform<double,3> m_AffineTransform; //... minc::write_linear_xfm(output_xfm, m_AffineTransform->GetMatrix(), m_AffineTransform->GetOffset()); Reading affine transformation from .xfm file itk::AffineTransform<double,3> m_AffineTransform; //... itk::Matrix<double,3,3> rotation; itk::Vector<double,3> translation; read_linear_xfm(input_xfm,rotation,translation); //... m_AffineTransform.SetOffset(translation); m_AffineTransform.SetMatrix(rotation); reading/writing .tag files std::vector<int> labels; std::vector<itk::Point<double>,3> tags; read_tags(tags, labels, input_tag); //.... write_tags(tags, labels, ouput_tag);