MINC/SoftwareDevelopment/EZMINC/ITK Integration
Better MINC1/2 support for ITK
editIf 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
editCompile 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
editCode from itk_dti.cpp from examples:
Using minc XFM files
edit- 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);