omni.interfaces.ants#

Functions

`N4BiasFieldCorrection`(out_file, in_file[, ...])	Bias Field Correction.
`antsApplyTransform`(prefix, reference, ...[, ...])	Apply a transform with antsApplyTransforms.
`antsRegistration`(warp_prefix, reference, source)	antsRegistration interface for Ants Syn Warp

omni.interfaces.ants.N4BiasFieldCorrection(out_file: str, in_file: str, bspline_fit: Optional[str] = None, other_args: Optional[str] = None)[source]#

Bias Field Correction.

Parameters:

out_file: str: Bias field corrected file.
in_file: str: File to bias field correct.
bspline_fit: str: Custom spline fit string.
other_args: str: Other arguments to pass in.

omni.interfaces.ants.antsApplyTransform(prefix: str, reference: str, source: str, transforms: Union[List, str], composite_warp: bool = False, other_args: Optional[str] = None)[source]#

Apply a transform with antsApplyTransforms.

Parameters:

prefix: str: Prefix of output image/warp
reference: str: Reference image to transform.
source: str: Source image to transform.
transforms: Union[List, str]: String of transforms to apply.
composite_warp: bool: Boolean indicating whether to output the image (False) or warp (True).
other_args: str: Other arguments to pass in.

omni.interfaces.ants.antsRegistration(warp_prefix: str, reference: str, source: str, warped: Optional[str] = None, inverse_warped: Optional[str] = None, grad_step: float = 1, update_field_var: float = 0, total_field_var: float = 0, metric: str = 'CC', rad_bin: int = 10, convergence: str = '500x200x200x0', threshold: float = 1e-06, threshold_window: int = 15, smoothing: str = '2x1x0x0', shrink_factors: str = '4x3x2x1', restrict_deform: str = '1x1x1', reference_mask: Optional[str] = None, source_mask: Optional[str] = None, initial_warp: Optional[str] = None, other_args: Optional[str] = None)[source]#

antsRegistration interface for Ants Syn Warp

Parameters:

warp_prefix: str: Prefix of output warp.
reference: str: Reference image to align.
source: str: Source image to align.
warped: str: Warped source image.
inverse_warped: str: Inverse Warped reference image.
grad_step: float: Gradient step size for optimization.
update_field_var: float: Update field variance for Syn algorithm.
total_field_var: float: Total field variance for SyN algorithm.
metric: str: Optimization metric to use.
rad_bin: int: Radius or number of bins of metric.
convergence: str: Number of iterations to use at each level of optimization.
threshold: float: Stopping criterion for optimization.
threshold_window: int: Window size for optimization.
smoothing: str: Smoothing kernel size for each level of optimization.
shrink_factors: str: Resampling factor for each level of optimization.
restrict_deform: str: 1 to allow warp in a direction; 0 to restrict warp in a direction.
reference_mask: str: Path to a reference extent mask.
source_mask: str: Path to a source extent mask.
initial_warp: str: Initializes SyN registration with a warp.
other_args: str: Other arguments to pass in.