omni.interfaces.afni#

Functions

`Allineate`(prefix, base, source[, cost, ...])	3dAllineate.
`Autobox`(prefix, source[, npad])	3dAutobox.
`NwarpApply`(prefix, master, source, nwarp)	3dNwarpApply
`NwarpCat`(prefix, warps[, iwarps])	3dNwarpCat.
`cat_matvec`(concatenated_affine, affine_matrices)	Concatenate affine transforms.
`resample`(prefix, master, source[, rmode, dxyz])	3dresample

omni.interfaces.afni.Allineate(prefix: str, base: str, source: str, cost: Optional[str] = None, final: str = 'wsinc5', warp: Optional[str] = None, matrix_save: Optional[str] = None, matrix_apply: Optional[str] = None, fineblur: Optional[int] = None, nmatch: Optional[str] = None, twopass: bool = False, other_args: Optional[str] = None)[source]#

3dAllineate.

Parameters:

prefix: str: Prefix for output image.
base: str: Reference image to align to.
source: str: Source image to align.
cost: str: Cost function to use.
final: str: Final interpolation method.
warp: str: Type of warp string (e.g. shift_rotate, shift_rotate_scale, etc).
matrix_save: str: Path to save affine matrix.
matrix_apply: str: Path to apply affine matrix.
fineblur: int: Size of fine blurring kernel to use.
nmatch: str: Percentage of voxels to match (e.g. “100%”).
twopass: bool: Do twopass registration.
other_args: str: Other arguments to pass in.

omni.interfaces.afni.Autobox(prefix: str, source: str, npad: Optional[int] = None)[source]#

3dAutobox.

Parameters:

prefix: str: Prefix for output image.
source: str: Input image.
npad: int: Padding.

omni.interfaces.afni.NwarpApply(prefix: str, master: str, source: str, nwarp: Union[List, str])[source]#

3dNwarpApply

Parameters:

prefix: str: Prefix for output image.
master: str: Reference image to align to.
source: str: Source image to align.
nwarp: Union[List, str]: List of transforms to apply.

omni.interfaces.afni.NwarpCat(prefix: str, warps: Union[List[str], str], iwarps: Union[List[bool], bool] = False)[source]#

3dNwarpCat.

Parameters:

prefix: str: Prefix for output warp.
warps: Union[List, str]: List of transforms to concatenate (or single transform string).
iwarps: Union[List, bool]: List of booleans to specify whether transform should be inverted (or singular boolean for single transform).

omni.interfaces.afni.cat_matvec(concatenated_affine: str, affine_matrices: str)[source]#

Concatenate affine transforms.

Parameters:

concatenated_affine: str: Concatenated affine matrix.
affine_matrices: str: String of affine matrices to concatenate.

omni.interfaces.afni.resample(prefix: str, master: str, source: str, rmode: str = 'Cu', dxyz: Optional[float] = None)[source]#

3dresample

Parameters:

prefix: str: Prefix for output image.
master: str: Reference Image.
source: str: Input image.
rmode: str: Interpolation mode.
dxyz: float: Resolution to resample to.