nighres.intensity.mp2rage_t1_mapping(first_inversion, second_inversion, inversion_times, flip_angles, inversion_TR, excitation_TR, N_excitations, efficiency=0.96, correct_B1=False, B1_map=None, scale_phase=True, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]

MP2RAGE T1 mapping

Estimate T1/R1 by a look-up table method adapted from [1]

  • first_inversion ([niimg]) – List of {magnitude, phase} images for the first inversion
  • second_inversion ([niimg]) – List of {magnitude, phase} images for the second inversion
  • inversion_times ([float]) – List of {first, second} inversion times, in seconds
  • flip_angles ([float]) – List of {first, second} flip angles, in degrees
  • inversion_TR (float) – Inversion repetition time, in seconds
  • excitation_TR ([float]) – List of {first,second} repetition times,in seconds
  • N_excitations (int) – Number of excitations
  • efficiency (float) – Inversion efficiency (default is 0.96)
  • correct_B1 (bool) – Whether to correct for B1 inhomogeneities (default is False)
  • B1_map (niimg) – Computed B1 map
  • scale_phase (bool) – Whether to rescale the phase image in [0,2PI] or to assume it is already in radians
  • 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)

  • t1 (niimg): Map of estimated T1 times (_qt1map-t1)
  • r1 (niimg): Map of estimated R1 relaxation rate (_qt1map-r1)
  • uni (niimg): Estimated PD weighted image at TE=0 (_qt1map-uni)

Return type:



Original Java module by Pierre-Louis Bazin.


[1]Marques, Kober, Krueger, van der Zwaag, Van de Moortele, Gruetter (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.