mp2rage_skullstripping

nighres.brain.mp2rage_skullstripping(second_inversion, t1_weighted=None, t1_map=None, skip_zero_values=True, topology_lut_dir=None, save_data=False, overwrite=False, output_dir=None, file_name=None, return_filename=False)[source]

MP2RAGE skull stripping

Estimates a brain mask from MRI data acquired with the MP2RAGE sequence. At least a T1-weighted or a T1 map image is required

Parameters:
  • second_inversion (niimg) – Second inversion image derived from MP2RAGE sequence
  • t1_weighted (niimg) – T1-weighted image derived from MP2RAGE sequence (also referred to as “uniform” image) At least one of t1_weighted and t1_map is required
  • t1_map (niimg) – Quantitative T1 map image derived from MP2RAGE sequence At least one of t1_weighted and t1_map is required
  • skip_zero_values (bool) – Ignores voxels with zero value (default is True)
  • 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)
  • return_filename (bool, optional) – Return filename instead of object
Returns:

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

  • brain_mask (niimg): Binary brain mask (_strip-mask)
  • inv2_masked (niimg): Masked second inversion imamge (_strip-inv2)
  • t1w_masked (niimg): Masked T1-weighted image (_strip-t1w)
  • t1map_masked (niimg): Masked T1 map (_strip-t1map)

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