Convert between the old format fixel image (.msf / .msh) and the new fixel directory format


fixelconvert [ options ]  fixel_in fixel_out
  • fixel_in: the input fixel file / directory.
  • fixel_out: the output fixel file / directory.


Options for converting from old to new format

  • -name string assign a different name to the value field output (Default: value). Do not include the file extension.
  • -nii output the index, directions and data file in NIfTI format instead of .mif
  • -out_size also output the ‘size’ field from the old format
  • -template path specify an existing fixel directory (in the new format) to which the new output should conform

Options for converting from new to old format

  • -value path nominate the data file to import to the ‘value’ field in the old format
  • -in_size path import data for the ‘size’ field in the old format

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 ( and 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.

For more details, see