embedded_antsreg_2d¶
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nighres.registration.
embedded_antsreg_2d
(source_image, target_image, run_rigid=False, rigid_iterations=1000, run_affine=False, affine_iterations=1000, run_syn=True, coarse_iterations=40, medium_iterations=50, fine_iterations=40, scaling_factor=32, cost_function='MutualInformation', interpolation='NearestNeighbor', regularization='High', convergence=1e-06, mask_zero=False, ignore_affine=False, ignore_header=False, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ Embedded ANTS Registration 2D
Runs the rigid and/or Symmetric Normalization (SyN) algorithm of ANTs and formats the output deformations into voxel coordinate mappings as used in CBSTools registration and transformation routines.
Parameters: - source_image (niimg) – Image to register
- target_image (niimg) – Reference image to match
- run_rigid (bool) – Whether or not to run a rigid registration first (default is False)
- rigid_iterations (float) – Number of iterations in the rigid step (default is 1000)
- run_affine (bool) – Whether or not to run a affine registration first (default is False)
- affine_iterations (float) – Number of iterations in the affine step (default is 1000)
- run_syn (bool) – Whether or not to run a SyN registration (default is True)
- coarse_iterations (float) – Number of iterations at the coarse level (default is 40)
- medium_iterations (float) – Number of iterations at the medium level (default is 50)
- fine_iterations (float) – Number of iterations at the fine level (default is 40)
- cost_function ({'CrossCorrelation', 'MutualInformation'}) – Cost function for the registration (default is ‘MutualInformation’)
- interpolation ({'NearestNeighbor', 'Linear'}) – Interpolation for the registration result (default is ‘NearestNeighbor’)
- convergence (flaot) – Threshold for convergence, can make the algorithm very slow (default is convergence)
- ignore_affine (bool) – Ignore the affine matrix information extracted from the image header (default is False)
- ignore_header (bool) – Ignore the orientation information and affine matrix information extracted from the image header (default is False)
- save_data (bool) – Save output data to file (default is False)
- overwrite (bool) – Overwrite existing results (default is False)
- output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
- file_name (str, optional) – Desired base name for output files with file extension (suffixes will be added)
Returns: Dictionary collecting outputs under the following keys (suffix of output files in brackets)
- transformed_source (niimg): Deformed source image (_ants-def)
- mapping (niimg): Coordinate mapping from source to target (_ants-map)
- inverse (niimg): Inverse coordinate mapping from target to source (_ants-invmap)
Return type: Notes
Port of the CBSTools Java module by Pierre-Louis Bazin. The main algorithm is part of the ANTs software by Brian Avants and colleagues [1]. Parameters have been set to values commonly found in neuroimaging scripts online, but not necessarily optimal.
References
[1] Avants et al (2008), Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain, Med Image Anal. 12(1):26-41