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.
  • -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)
  • -failonwarn terminate program if a warning is produced
  • -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) 2008-2017 the MRtrix3 contributors.

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