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ToOrientation

ToOrientation

Bases: SpatialTransform

Reorient the data to a specified orientation.

This transform reorders the voxels and modifies the affine matrix to match the specified orientation code. The image intensity values are not modified, and the sample locations in the scanner space are preserved.

Common orientation codes include:

  • 'RAS' (neurological convention):
    • The first axis goes from Left to Right (R).
    • The second axis goes from Posterior to Anterior (A).
    • The third axis goes from Inferior to Superior (S).
  • 'LAS' (radiological convention):
    • The first axis goes from Right to Left (L).
    • The second axis goes from Posterior to Anterior (A).
    • The third axis goes from Inferior to Superior (S).

See NiBabel docs about image orientation for more information.

Parameters:

Name Type Description Default
orientation str

A three-letter orientation code. Examples: 'RAS', 'LAS', 'LPS', 'PLS', 'SLP'. The code must contain one character for each axis direction: R or L, A or P, and S or I.

 'RAS'
**kwargs

See Transform for additional keyword arguments.

 {}

__call__(data) 

__call__(data: Subject) -> Subject

__call__(data: ImageT) -> ImageT

__call__(data: torch.Tensor) -> torch.Tensor

__call__(data: np.ndarray) -> np.ndarray

__call__(data: sitk.Image) -> sitk.Image

__call__(data: dict[str, object]) -> dict[str, object]

__call__(data: nib.Nifti1Image) -> nib.Nifti1Image

Transform data and return a result of the same type.

Parameters:

Name Type Description Default
data TypeTransformInput

Instance of torchio.Subject, 4D torch.Tensor or numpy.ndarray with dimensions \((C, W, H, D)\), where \(C\) is the number of channels and \(W, H, D\) are the spatial dimensions. If the input is a tensor, the affine matrix will be set to identity. Other valid input types are a SimpleITK image, a torchio.Image, a NiBabel Nifti1 image or a dict. The output type is the same as the input type.

 required

to_hydra_config()

Return a dictionary representation of the transform for Hydra instantiation.