Generate a fixel-fixel connectivity matrix


fixelconnectivity [ options ]  fixel_directory tracks matrix
  • fixel_directory: the directory containing the fixels between which connectivity will be quantified

  • tracks: the tracks used to determine fixel-fixel connectivity

  • matrix: the output fixel-fixel connectivity matrix directory path


This command will generate a directory containing three images, which encodes the fixel-fixel connectivity matrix. Documentation regarding this format and how to use it will come in the future.


Options that influence generation of the connectivity matrix / matrices

  • -threshold value a threshold to define the required fraction of shared connections to be included in the neighbourhood (default: 0.01)

  • -angle value the max angle threshold for assigning streamline tangents to fixels (Default: 45 degrees)

  • -mask file provide a fixel data file containing a mask of those fixels to be computed; fixels outside the mask will be empty in the output 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.


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: Robert E. Smith (

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

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