Compute images statistics


mrstats [ options ]  image
  • image: the input image from which statistics will be computed.


Statistics options

  • -output field output only the field specified. Multiple such options can be supplied if required. Choices are: mean, median, std, min, max, count. Useful for use in scripts.
  • -mask image only perform computation within the specified binary mask image.
  • -ignorezero ignore zero values during statistics calculation

Additional options for mrstats

  • -allvolumes generate statistics across all image volumes, rather than one set of statistics per image volume

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).
  • -help display this information page and exit.
  • -version display version information and exit.

Author: J-Donald Tournier (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at

MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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