nifreeze.registration.utils module

Utilities to aid in performing and evaluating image registration.

This module provides functions to compute displacements of image coordinates under a transformation, useful for assessing the accuracy of image registration processes.

nifreeze.registration.utils.RADIUS = 50.0

Typical radius (in mm) of a sphere mimicking the size of a typical human brain.

nifreeze.registration.utils.compute_fd_from_motion(motion_parameters: ndarray, radius: float = 50.0) → ndarray

Compute framewise displacement (FD) from motion parameters.

Each row in the motion parameters represents one frame, and columns represent each coordinate axis x, y`, and z. Translation parameters are followed by rotation parameters column-wise.

Parameters:

• motion_parameters (numpy.ndarray) – Motion parameters.

• radius (float, optional) – Radius (in mm) of a sphere mimicking the size of a typical human brain.

Returns:

The framewise displacement (FD) as the sum of absolute differences between consecutive frames.

Return type:

numpy.ndarray

nifreeze.registration.utils.compute_fd_from_transform(img: nibabel.spatialimages.SpatialImage, test_xfm: nitransforms.base.TransformBase, radius: float = 50.0) → float

Compute the framewise displacement (FD) for a given transformation.

Parameters:

• img (SpatialImage) – The reference image. Used to extract the center coordinates.

• test_xfm (TransformBase) – The transformation to test. Applied to coordinates around the image center.

• radius (float, optional) – The radius (in mm) of the spherical neighborhood around the center of the image.

Returns:

The average framewise displacement (FD) for the test transformation.

Return type:

float

nifreeze.registration.utils.displacements_within_mask(mask_img: nb.spatialimages.SpatialImage, test_xfm: nt.base.TransformBase, reference_xfm: nt.base.TransformBase | None = None) → np.ndarray

Compute the distance between voxel coordinates mapped through two transforms.

Parameters:

• mask_img (SpatialImage) – A mask image that defines the region of interest. Voxel coordinates within the mask are transformed.

• test_xfm (TransformBase) – The transformation to test. This transformation is applied to the voxel coordinates.

• reference_xfm (TransformBase, optional) – A reference transformation to compare with. If None, the identity transformation is assumed (no transformation).

Returns:

An array of displacements (in mm) for each voxel within the mask.

Return type:

ndarray

nifreeze.registration.utils.extract_motion_parameters(affine: ndarray) → Tuple[ndarray, ndarray]

Extract translation (mm) and rotation (degrees) parameters from an affine matrix.

Parameters:

affine (ndarray) – The affine transformation matrix.

Returns:

Extracted translation and rotation parameters.

Return type:

tuple