probtrackx2 is the FMRIB Software Library (FSL) probabilistic fiber tracking tool using diffusion MRI.

This modification adds some functionality to enforce the initial tracking direction. For example, one might want the first fiber propagation step to move in the normal direction to the surface, seeded at a vertex. The default FSL probtrackx2 tool allows one to specify an initial fiber bundle compartment from which it then samples the initial propgation direction (--fibst) -- however, one cannot explicitly enfore the first step direction. For a full view of all default FSL options, have a look at the probtrackxOptions.h file.

The class Particle (defined in particle.h), performs the meat of the tracking. A Particle object performs the fiber tracking for a single streamline, for a single seed. At each step of the streamline propagation, Particle samples a spherical coordinate (azimuthal angle, polar angle, fiber comparment) from the 3D diffusion model generated by bedpostx, checks that some constraints are applied, and moves in that direction using a Particle.jump(...) member function. Here, I provide an edit to accept an initial azimuthal and polar angles to enforce the first step.

Likewise, I also combine some work by St.-Onge et al. to add functionality for using surface curvature to enhance tractography results. The bulk of these modifications are included in seed_utils.h. More notes to come...