Compute fixel-wise or voxel-wise metrics from a 4D deformation field


warp2metric [ options ]  in
  • in: the input deformation field


  • -fc template_fixel_directory output_fixel_directory output_fixel_data use an input template fixel image to define fibre orientations and output a fixel image describing the change in fibre cross-section (FC) in the perpendicular plane to the fixel orientation. e.g. warp2metric warp.mif -fc fixel_template_directory output_fixel_directory fc.mif
  • -jmat output output a Jacobian matrix image stored in column-major order along the 4th dimension.Note the output jacobian describes the warp gradient w.r.t the scanner space coordinate system
  • -jdet output output the Jacobian determinant instead of the full matrix

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.


Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway, GR. Connelly, A.Investigating White Matter Fibre Density and Morphology using Fixel-Based Analysis. Neuroimage, 2016, 10.1016/j.neuroimage.2016.09.029

Author: David Raffelt (david.raffelt@florey.edu.au)

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 http://mozilla.org/MPL/2.0/

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 http://www.mrtrix.org/