# 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).
• -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

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