Workflow for Local Fiber Tracking.

This workflow use 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.
tracking_method : string, optional
Select direction getter strategy:
  • “eudx” (Uses the peaks saved in the pam_files)
  • “deterministic” or “det” for a deterministic tracking (Uses the sh saved in the pam_files, default)
  • “probabilistic” or “prob” for a Probabilistic tracking (Uses the sh saved in the pam_files)
  • “closestpeaks” or “cp” for a ClosestPeaks tracking (Uses the sh saved in the pam_files)
pmf_threshold : float, optional
Threshold for ODF functions. (default 0.1)
max_angle : float, optional
Maximum angle between tract segments. This angle can be more generous (larger) than values typically used with probabilistic direction getters. The angle range is (0, 90)
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.