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


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


Fixel data are stored utilising the fixel directory format described in the main documentation, which can be found at the following link:


  • -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.

  • -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).

  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.

  • -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, 2017, 144, 58-73. doi: 10.1016/j.neuroimage.2016.09.029

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

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

Copyright: Copyright (c) 2008-2024 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/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.