cmind.pipeline.ants_register¶
utility for calling antsRegistration
Functions
ants_register (fixed, moving, output_dir, ...) |
utility to call antsRegistration |
-
cmind.pipeline.ants_register.
ants_register
(fixed, moving, output_dir, output_root, ANTS_path=None, operation_type='both', initial_COM_alignment=True, use_Bspline_SyN=False, registration_mask_fixed=None, registration_mask_moving=None, affine_only=False, rigid_affine=False, concat_transforms=True, dim=3, interp_type='Linear', nopng=False, precision_case='lenient', initial_transform_list=None, verbose=False, logger=None)[source]¶ utility to call antsRegistration
Parameters: fixed : str
image filename for the fixed image (registration target)
moving : str
image filename for the moving image
output_dir : str
path to store the output
output_root : str
filenames of the transforms will be ${output_dir}/${output_root}0GenericAffine.mat, etc
ANTS_path : str
path to the ants binaries
operation_type : {“compute”,”apply”,”both”}, optional
compute = compute registration only, apply = apply existing registration only, both = compute & apply registration
initial_COM_alignment : bool, optional
align center of mass of the volumes prior to other registration stages?
use_Bspline_SyN : bool, optional
use B-Spline variant of SyN instead
registration_mask_fixed : str, optional
filename of binary weight mask to be applied to fixed image during registration
registration_mask_moving : str, optional
filename of binary weight mask to be applied to moving image during registration
affine_only : bool, optional
If true, only do a linear, affine transformation
rigid_affine : bool, optional
If true, do only a rigid registration
concat_transforms : bool, optional
concatenate transforms
dim : {2, 3}, optional
number of image dimensions
interp_type : str, optional
interpolation type
nopng : bool, optional
if False, generate overlay images summarizing the registration
precision_case : {‘defacer’,’lenient’,’ants_default’,’strict’}, optional
choose from preset precision levels for the registrations
initial_transform_list : list of str, optional
initialize the registrtion using this list of transforms
verbose : bool, optional
print additional output (to terminal and log)
logger : logging.Logger or str, optional
logging.Logger object (or string of a filename to log to)
Returns: warp_file : str
file containing the calculated warp
aff_file : str
file containing the calculated affine transform
output_warped : str
file containing the warped image
Notes
- Possible interp_type strings are:
- HammingWindowedSinc
- NearestNeighbor
- BSpline[<order=3>]
- MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
- Gaussian[<sigma=imageSpacing>,<alpha=1.0>]
- CosineWindowedSinc
- WelchWindowedSinc
- HammingWindowedSinc
- LanczosWindowedSinc
- “”