Convert a fixel-based sparse-data image into an spherical harmonic image


fixel2sh [ options ]  fixel_in sh_out
  • fixel_in: the input fixel data file.
  • sh_out: the output sh image.


This command generates spherical harmonic data from fixels that can be visualised using the ODF tool in MRview. The output ODF lobes are scaled according to the values in the input fixel image.


  • -lmax order set the maximum harmonic order for the output series (Default: 8)

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 ( & David Raffelt (

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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