mp2rage_dura_estimation

nighres.brain.mp2rage_dura_estimation(second_inversion, skullstrip_mask, background_distance=5.0, output_type='dura_region', save_data=False, overwrite=False, output_dir=None, file_name=None, return_filename=False)[source]

MP2RAGE dura estimation

Filters a MP2RAGE brain image to obtain a probability map of dura matter.

Parameters:
  • second_inversion (niimg) – Second inversion image derived from MP2RAGE sequence
  • skullstrip_mask (niimg) – Skullstripping mask defining the approximate region including the brain
  • background_distance (float) – Maximum distance within the mask for dura (default is 5.0 mm)
  • output_type ({'dura_region','boundary','dura_prior','bg_prior',) – ‘intens_prior’} Type of output result (default is ‘dura_region’)
  • 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 of output files in brackets)

  • result (niimg): Dura probability image (_dura-proba)

Return type:

dict

Notes

Original Java module by Pierre-Louis Bazin. Details on the algorithm can be found in [1] and a presentation of the MP2RAGE sequence in [2]

References

[1]Bazin et al. (2014). A computational framework for ultra-high resolution cortical segmentation at 7 Tesla. DOI: 10.1016/j.neuroimage.2013.03.077
[2]Marques et al. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. DOI: 10.1016/j.neuroimage.2009.10.002