Multi-Tissue Bias field correction and Intensity Normalisation (MTBIN)


mtbin [ options ]  input output [ input output ... ]
  • input output: list of all input and output tissue compartment files. See example usage in the description. Note that any number of tissues can be normalised


This command inputs N number of tissue components (e.g. from multi-tissue CSD), and outputs N corrected tissue components. Intensity normalisation is performed by either determining a common global normalisation factor for all tissue types (default) or by normalising each tissue type independently with a single tissue-specific global scale factor.

Example usage: mtbin wm.mif wm_norm.mif gm.mif gm_norm.mif csf.mif csf_norm.mif.

The estimated multiplicative bias field is guaranteed to have a mean of 1 over all voxels within the mask.


  • -mask image define the mask to compute the normalisation within. If not supplied this is estimated automatically
  • -value number specify the value to which the summed tissue compartments will be normalised to (Default: sqrt(1/(4*pi)) = 0.282094)
  • -bias image output the estimated bias field
  • -independent intensity normalise each tissue type independently
  • -maxiter number set the maximum number of iterations. Default(100). It will stop before the max iterations if convergence is detected
  • -check image check the automatically computed mask

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status.
  • -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)
  • -failonwarn terminate program if a warning is produced
  • -help display this information page and exit.
  • -version display version information and exit.

Author: David Raffelt (

Copyright: Copyright (c) 2008-2017 the MRtrix3 contributors

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