NIfTI
Implementation Details
Note
The NIfTI crate only support NIfTI-1 formats. LUMA therefore does not support NIfTI-2 formats at this time.
NIfTI files are supported as image formats through the nifti crate,
which provides a Rust interface for reading and writing NIfTI files.
The library supports both ASCII and binary formats.
LUMA supports loading nii and nii.gz files.
NIfTI maps normally to a RAS (Right-Anterior-Superior) coordinate system, which is a common convention in neuroimaging, however LUMA uses the LPS (Left-Posterior-Superior) coordinate system. So when loading NIfTI files, LUMA automatically converts the coordinates from RAS to LPS to maintain consistency with its internal representation.
let x: Vec<f64> = (0..nx).map(|i| -{affine[(0, 0)] * i as f64 + affine[(0, 3)]}).collect(); // Negative to convert from RAS to LPS
let y: Vec<f64> = (0..ny).map(|i| -{affine[(1, 1)] * i as f64 + affine[(1, 3)]}).collect(); // Negative to convert from RAS to LPS
let z: Vec<f64> = (0..nz).map(|i| affine[(2, 2)] * i as f64 + affine[(2, 3)]).collect(); // No change needed for Z-axis as it is the same in both RAS and LPS
We would recommend you check your model and image data to ensure that the coordinate system is correctly interpreted using the --visualise or --visualise align flags.