volumetric_layering¶
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nighres.laminar.
volumetric_layering
(inner_levelset, outer_levelset, n_layers=4, topology_lut_dir=None, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ Equivolumetric layering of the cortical sheet.
Parameters: - inner_levelset (niimg) – Levelset representation of the inner surface, typically GM/WM surface
- outer_levelset (niimg) – Levelset representation of the outer surface, typically GM/CSF surface
- n_layers (int, optional) – Number of layers to be created (default is 10)
- topology_lut_dir (str, optional) – Path to directory in which topology files are stored (default is stored in TOPOLOGY_LUT_DIR)
- 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)
- depth (niimg): Continuous depth from 0 (inner surface) to 1 (outer surface) (_layering-depth)
- layers (niimg): Discrete layers from 1 (bordering inner surface) to n_layers (bordering outer surface) (_layering-layers)
- boundaries (niimg): Levelset representations of boundaries between all layers in 4D (_layering-boundaries)
Return type: Notes
Original Java module by Miriam Waehnert, Pierre-Louis Bazin and Juliane Dinse. Algorithm details can be found in [1]
References
[1] Waehnert et al (2014) Anatomically motivated modeling of cortical laminae. DOI: 10.1016/j.neuroimage.2013.03.078