Multi-tissue normalise


mtnormalise [ 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


Globally normalise multiple tissue compartments (e.g. WM, GM, CSF) from multi-tissue CSD such that their sum (of their DC terms) within each voxel is as close to a scalar as possible (Default: sqrt(1/(4*pi)). Normalisation is performed by solving for a single scale factor to adjust each tissue type.

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


  • -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 to (Default: sqrt(1/(4*pi) = 0.282)

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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