nighres.laminar.volumetric_layering(inner_levelset, outer_levelset, n_layers=4, topology_lut_dir=None, method='volume-preserving', layer_dir='outward', curv_scale=3, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]

Equivolumetric layering of the cortical sheet.

  • 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)
  • method (str) – Which model to use, either “volume-preserving” or “distance-preserving” (default is “volume-preserving”)
  • layer_dir (str) – Direction to perform the layering, either “outward” or “inward” (default is “outward”)
  • curv_scale (int) – Scale of the curvature approximation window in voxels (default is 3, computation may become very slow for higher values)
  • 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)

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:



Original Java module by Miriam Waehnert, Pierre-Louis Bazin and Juliane Dinse. Algorithm details can be found in [1]


[1]Waehnert et al (2014) Anatomically motivated modeling of cortical laminae. DOI: 10.1016/j.neuroimage.2013.03.078

Examples using nighres.laminar.volumetric_layering