Create bitwise image by thresholding image intensity


mrthreshold [ options ]  input output
  • input: the input image to be thresholded.
  • output: the output binary image mask.


By default, an optimal threshold is determined using a parameter-free method. Alternatively the threshold can be defined manually by the user.


  • -abs value specify threshold value as absolute intensity.
  • -percentile value threshold the image at the ith percentile.
  • -top N provide a mask of the N top-valued voxels
  • -bottom N provide a mask of the N bottom-valued voxels
  • -invert invert output binary mask.
  • -toppercent N provide a mask of the N%% top-valued voxels
  • -bottompercent N provide a mask of the N%% bottom-valued voxels
  • -nan use NaN as the output zero value.
  • -ignorezero ignore zero-valued input voxels.
  • -mask image compute the optimal threshold based on voxels within a mask.

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.


  • If not using any manual thresholding option:Ridgway, G. R.; Omar, R.; Ourselin, S.; Hill, D. L.; Warren, J. D. & Fox, N. C. Issues with threshold masking in voxel-based morphometry of atrophied brains. NeuroImage, 2009, 44, 99-111

Author: J-Donald Tournier (

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

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