dirgen

Synopsis

Generate a set of uniformly distributed directions using a bipolar electrostatic repulsion model

Usage

dirgen [ options ]  ndir dirs
  • ndir: the number of directions to generate.
  • dirs: the text file to write the directions to, as [ az el ] pairs.

Description

Directions are distributed by analogy to an electrostatic repulsion system, with each direction corresponding to a single electrostatic charge (for -unipolar), or a pair of diametrically opposed charges (for the default bipolar case). The energy of the system is determined based on the Coulomb repulsion, which assumes the form 1/r^power, where r is the distance between any pair of charges, and p is the power assumed for the repulsion law (default: 1). The minimum energy state is obtained by gradient descent.

Options

  • -power exp specify exponent to use for repulsion power law (default: 1). This must be a power of 2 (i.e. 1, 2, 4, 8, 16, …).
  • -niter num specify the maximum number of iterations to perform (default: 10000).
  • -restarts num specify the number of restarts to perform (default: 10).
  • -unipolar optimise assuming a unipolar electrostatic repulsion model rather than the bipolar model normally assumed in DWI
  • -cartesian Output the directions in Cartesian coordinates [x y z] instead of [az el].

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.

References

Jones, D.; Horsfield, M. & Simmons, A. Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging. Magnetic Resonance in Medicine, 1999, 42: 515-525

Papadakis, N. G.; Murrills, C. D.; Hall, L. D.; Huang, C. L.-H. & Adrian Carpenter, T. Minimal gradient encoding for robust estimation of diffusion anisotropy. Magnetic Resonance Imaging, 2000, 18: 671-679


Author: J-Donald Tournier (jdtournier@gmail.com)

Copyright: Copyright (c) 2008-2019 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/.