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dipy_track_pft
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usage: dipy_track_pft [-h] [--step_size float] [--seed_density int]
                     [--pmf_threshold float] [--max_angle float]
                     [--pft_back float] [--pft_front float] [--pft_count int]
                     [--out_dir str] [--out_tractogram str] [--save_seeds]
                     pam_files wm_files gm_files csf_files seeding_files

Workflow for Particle Filtering Tracking.

This workflow use a saved peaks and metrics (PAM) file as input.

positional arguments:
  pam_files             Path to the peaks and metrics files. This path may contain  wildcards to use multiple masks at once.
  wm_files              Path to white matter partial volume estimate for tracking (CMC).
  gm_files              Path to grey matter partial volume estimate for tracking (CMC).
  csf_files             Path to cerebrospinal fluid partial volume estimate for tracking (CMC).
  seeding_files         A binary image showing where we need to seed for tracking.

optional arguments:
  -h, --help            show this help message and exit
  --step_size float     Step size used for tracking (default 0.2mm).
  --seed_density int    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
                        Threshold for ODF functions (default 0.1).
  --max_angle float     Maximum angle between streamline segments (range [0, 90], default 20).
  --pft_back float      Distance in mm to back track before starting the particle filtering tractography (default 2mm). The total particle filtering tractography distance is equal to back_tracking_dist + front_tracking_dist.
  --pft_front float     Distance in mm to run the particle filtering tractography after the the back track distance (default 1mm). The total particle filtering tractography distance is equal to back_tracking_dist + front_tracking_dist.
  --pft_count int       Number of particles to use in the particle filter (default 15).
  --save_seeds          If true, save the seeds associated to their streamline in the 'data_per_streamline' Tractogram dictionary using 'seeds' as the key

output arguments(optional):
  --out_dir str         Output directory (default input file directory)
  --out_tractogram str  Name of the tractogram file to be saved (default 'tractogram.trk')

References: 
Girard, G., Whittingstall, K., Deriche, R., & Descoteaux, M. Towardsquantitative connectivity analysis: reducing tractography biases.NeuroImage, 98, 266-278, 2014.
Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.