Workflow for deterministic using a saved peaks and metrics (PAM) file as input.


pam_files : string
Path to the peaks and metrics files. This path may contain
wildcards to use multiple masks at once.
stopping_files : string
Path of FA or other images used for stopping criteria for tracking.
seeding_files : string
A binary image showing where we need to seed for tracking.
stopping_thr : float, optional
Threshold applied to stopping volume’s data to identify where
tracking has to stop (default 0.25).
seed_density : int, optional
Number of seeds per dimension inside voxel (default 1).
For example, seed_density of 2 means 8 regularly distributed points in the voxel. And seed density of 1 means 1 point at the center of the voxel.
use_sh : bool, optional
Use spherical harmonics saved in peaks to find the
maximum peak cone. (default False)
out_dir : string, optional
Output directory (default input file directory)
out_tractogram : string, optional
Name of the tractogram file to be saved (default ‘tractogram.trk’)


Garyfallidis, University of Cambridge, PhD thesis 2012. Amirbekian, University of California San Francisco, PhD thesis 2017.