simple_skeleton¶
-
nighres.shape.
simple_skeleton
(input_image, shape_image_type='signed_distance', boundary_threshold=0.0, skeleton_threshold=2.0, topology_lut_dir=None, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ Simple Skeleton
Create a skeleton for a levelset surface or a probability map (loosely adapted from Bouix et al., 2006)
Parameters: - input_image (niimg) – Image containing structure-of-interest
- shape_image_type (str) – Shape of the input image: either ‘signed_distance’ or ‘probability_map’.
- boundary_threshold (float) – Boundary threshold (>0: inside, <0: outside)
- skeleton_threshold (float) – Skeleton threshold (>0: inside, <0: outside)
- topology_lut_dir (str) – Directory of LUT topology
- save_data (bool, optional) – Save output data to file (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)
- medial (niimg): A 2D medial surface extracted from the shape (_ssk-med)
- skeleton (niimg): The 1D skeleton extracted from the shape (_ssk-skel)
Return type: Notes
Original Java module by Pierre-Louis Bazin.