LocalFiberTrackingPAMFlow

Parameters

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’)

References

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