Generate a histogram of image intensities


mrhistogram [ options ]  image hist
  • image: the input image from which the histogram will be computed
  • hist: the output histogram file


Histogram generation options

  • -bins num Manually set the number of bins to use to generate the histogram.
  • -template file Use an existing histogram file as the template for histogram formation
  • -mask image Calculate the histogram only within a mask image.
  • -ignorezero ignore zero-valued data during histogram construction.

Additional options for mrhistogram

  • -allvolumes generate one histogram across all image volumes, rather than one 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: Robert E. Smith (

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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