filter_stacking

nighres.brain.filter_stacking(dura_img=None, pvcsf_img=None, arteries_img=None, save_data=False, overwrite=False, output_dir=None, file_name=None, return_filename=False)[source]

Filter stacking

A small utility to combine multiple priors derived from filtering of the CSF partial voluming, arteries, and/or remaining dura mater. The filter priors (in [0,1]) are arranged in a specific way (in increments of 2) that is expected by the Filters contrast type in MGDM

Parameters:
  • dura_img (niimg, optional) – Prior for the location of remaining dura mater after skull stripping. At least one prior image is required
  • pvcsf_img (niimg, optional) – Prior for the location of CSF partial voluming (mostly in sulcal regions). At least one prior image is required
  • arteries_img (niimg, optional) – Prior for the location of arteries, visible e.g. in MP2RAGE images. At least one prior image is required
  • 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)
  • return_filename (bool, optional) – Return filename instead of object
Returns:

Dictionary collecting outputs under the following keys (suffix in brackets)

  • result (niimg): Combined image, where only the strongest priors are kept (_bfs-img)

Return type:

dict

Notes

Original Java module by Pierre-Louis Bazin.