Modify the intensities of one image to match the histogram of another


mrhistmatch [ options ]  type input target output
  • type: type of histogram matching to perform; options are: scale,linear,nonlinear
  • input: the input image to be modified
  • target: the input image from which to derive the target histogram
  • output: the output image


Image masking options

  • -mask_input image only generate input histogram based on a specified binary mask image
  • -mask_target image only generate target histogram based on a specified binary mask image

Non-linear histogram matching options

  • -bins num the number of bins to use to generate the histograms

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
  • -debug display debugging messages.
  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).
  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
  • -help display this information page and exit.
  • -version display version information and exit.


  • If using inverse contrast normalization for inter-modal (DWI - T1) registration:
    Bhushan, C.; Haldar, J. P.; Choi, S.; Joshi, A. A.; Shattuck, D. W. & Leahy, R. M. Co-registration and distortion correction of diffusion and anatomical images based on inverse contrast normalization. NeuroImage, 2015, 115, 269-280

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: Robert E. Smith (

Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.

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