Sofa CGAL: meshing from medical images

[alvarez-pa]

Hello Sofa community,

I would like to use the Sofa CGAL plugin to create a mesh from labeled medical image data. I've seen the cube meshing example here, where a .inr image is used as input.

Is there a way to use other medical image formats such as NIfTI or MetaImage as input ? Or, is there a way to convert from these formats to the .inr format required by CGAL ? Medical images typically come in these formats.

Best

[alxbilger]

The example you mention is hosted here: https://github.com/sofa-framework/CGALPlugin/blob/master/scenes/MeshGenerationFromImage.scn

The image is loaded in the ImageContainer component, where you can specify a filename. Have you tried to specify a path to a NIfTI file? It should work. SOFA will consider files with .hdr and .nii as NIfTI images:

sofa/applications/plugins/image/ImageContainer.h

Lines 189 to 196 in 376a975

	else if (fname.find(".hdr")!=std::string::npos || fname.find(".nii")!=std::string::npos)
	{
	float voxsize[3];
	wimage->getCImgList().push_back(cimg_library::CImg<T>().load_analyze(fname.c_str(),voxsize));
	if (!container->transformIsSet)
	for(unsigned int i=0;i<3;i++) wtransform->getScale()[i]=(Real)voxsize[i];
	readNiftiHeader(container, fname);
	}

[alvarez-pa]

Thank you @alxbilger for your answer.

I had tried meshing from a MetaImage .mha file with no success. To try your suggestion, I converted the image to the NIfTI format and it worked ! The data type of the image needs to be unsigned char though, otherwise the ImageContainer component fails loading the image and throws a CImgIOException exception.

[hugtalbot]

Thanks a lot for the feedback @alvarez-pa
Would this make sense for you to contribute your change ?

[alvarez-pa]

@hugtalbot, there's no contribution as I did not need to make any code changes to SOFA. I simply used 3D Slicer for the image format conversion and casting.