Crop/remove fixels from sparse fixel image using a binary fixel mask


fixelcrop [ options ]  input_fixel_directory input_fixel_mask output_fixel_directory
  • input_fixel_directory: input fixel directory, all data files and directions file will be cropped and saved in the output fixel directory
  • input_fixel_mask: the input fixel data file defining which fixels to crop. Fixels with zero values will be removed
  • output_fixel_directory: the output directory to store the cropped directions and data files


The mask must be input as a fixel data file the same dimensions as the fixel data file(s) to be cropped.


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: David Raffelt ( & Rami Tabarra (

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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