fixelthreshold [ options ]  fixel_in threshold fixel_out
  • fixel_in: the input fixel image.
  • threshold: the input threshold
  • fixel_out: the output fixel image


Threshold the values in a fixel image


  • -crop remove fixels that fall below threshold (instead of assigning their value to zero or one)
  • -invert invert the output image (i.e. below threshold fixels are included instead)

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) 2008-2016 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

MRtrix 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.

For more details, see