PFTrackingPAMFlow
Workflow for Particle Filtering Tracking.
This workflow use a saved peaks and metrics (PAM) file as input.
Parameters
- pam_files : string
- Path to the peaks and metrics files. This path may contain
- wildcards to use multiple masks at once.
- wm_files : string
- Path of White matter for stopping criteria for tracking.
- gm_files : string
- Path of grey matter for stopping criteria for tracking.
- csf_files : string
- Path of cerebrospinal fluid for stopping criteria for tracking.
- seeding_files : string
- A binary image showing where we need to seed for tracking.
- step_size : float, optional
- Step size used for tracking.
- back_tracking_dist : float, optional
- Distance in mm to back track before starting the particle filtering
tractography. The total particle filtering tractography distance is
equal to back_tracking_dist + front_tracking_dist.
By default this is set to 2 mm.
- front_tracking_dist : float, optional
- Distance in mm to run the particle filtering tractography after the
the back track distance. The total particle filtering tractography
distance is equal to back_tracking_dist + front_tracking_dist. By
default this is set to 1 mm.
- max_trial : int, optional
- Maximum number of trial for the particle filtering tractography
(Prevents infinite loops, default=20).
- particle_count : int, optional
- Number of particles to use in the particle filter. (default 15)
- 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.
- 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
- Girard, G., Whittingstall, K., Deriche, R., & Descoteaux, M.
- Towards quantitative connectivity analysis: reducing
tractography biases. NeuroImage, 98, 266-278, 2014..