.. _scil_tracking_pft:

scil_tracking_pft
=================

::

	usage: __main__.py [-h] [--algo {det,prob}] [--step STEP_SIZE]
	                   [--min_length MIN_LENGTH] [--max_length MAX_LENGTH]
	                   [--theta THETA] [--act] [--sfthres SF_THRESHOLD]
	                   [--sfthres_init SF_THRESHOLD_INIT]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [--npv NPV | --nt NT] [--particles PARTICLES]
	                   [--back BACK_TRACKING] [--forward FORWARD_TRACKING] [--all]
	                   [--seed SEED] [-f] [--save_seeds]
	                   [--compress [COMPRESS_TH]]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_sh in_seed in_map_include map_exclude_file
	                   out_tractogram
	
	Local streamline HARDI tractography including Particle Filtering tracking.
	
	WARNING: This script DOES NOT support asymetric FODF input (aFODF).
	
	The tracking is done inside partial volume estimation maps and uses the
	particle filtering tractography (PFT) algorithm. See
	scil_tracking_pft_maps to generate PFT required maps.
	
	Streamlines longer than min_length and shorter than max_length are kept.
	The tracking direction is chosen in the aperture cone defined by the
	previous tracking direction and the angular constraint.
	Default parameters as suggested in [1].
	
	Algo 'det': the maxima of the spherical function (SF) the most closely aligned
	to the previous direction.
	Algo 'prob': a direction drawn from the empirical distribution function defined
	from the SF.
	
	For streamline compression, a rule of thumb is to set it to 0.1mm for the
	deterministic algorithm and 0.2mm for probabilitic algorithm.
	
	All the input nifti files must be in isotropic resolution.
	
	-----------------------------------------------------------------------------
	Reference:
	[1] Girard, G., Whittingstall K., Deriche, R., and Descoteaux, M. (2014).
	    Towards quantitative connectivity analysis: reducing tractographybiases.
	    Neuroimage.
	-----------------------------------------------------------------------------
	
	positional arguments:
	  in_sh                 Spherical harmonic file (.nii.gz).
	  in_seed               Seeding mask (.nii.gz).
	  in_map_include        The probability map (.nii.gz) of ending the
	                        streamline and including it in the output (CMC, PFT [1])
	  map_exclude_file      The probability map (.nii.gz) of ending the
	                        streamline and excluding it in the output (CMC, PFT [1]).
	  out_tractogram        Tractogram output file (must be .trk or .tck).
	
	Generic options:
	  -h, --help            show this help message and exit
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	
	Tracking options:
	  --algo {det,prob}     Algorithm to use (must be "det" or "prob"). [prob]
	  --step STEP_SIZE      Step size in mm. [0.2]
	  --min_length MIN_LENGTH
	                        Minimum length of a streamline in mm. [10.0]
	  --max_length MAX_LENGTH
	                        Maximum length of a streamline in mm. [300.0]
	  --theta THETA         Maximum angle between 2 steps. ["det"=45, "prob"=20]
	  --act                 If set, uses anatomically-constrained tractography (ACT) 
	                        instead of continuous map criterion (CMC).
	  --sfthres SF_THRESHOLD
	                        Spherical function relative threshold. [0.1]
	  --sfthres_init SF_THRESHOLD_INIT
	                        Spherical function relative threshold value for the 
	                        initial direction. [0.5]
	  --sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}
	                        Spherical harmonics basis used for the SH coefficients. 
	                        Must be either descoteaux07', 'tournier07', 
	                        'descoteaux07_legacy' or 'tournier07_legacy' [['descoteaux07_legacy']]:
	                            'descoteaux07'       : SH basis from the Descoteaux et al.
	                                                   MRM 2007 paper
	                            'tournier07'         : SH basis from the new Tournier et al.
	                                                   NeuroImage 2019 paper, as in MRtrix 3.
	                            'descoteaux07_legacy': SH basis from the legacy Dipy implementation
	                                                   of the Descoteaux et al. MRM 2007 paper
	                            'tournier07_legacy'  : SH basis from the legacy Tournier et al.
	                                                   NeuroImage 2007 paper.
	
	Seeding options:
	  When no option is provided, uses --npv 1.
	
	  --npv NPV             Number of seeds per voxel.
	  --nt NT               Total number of seeds to use.
	
	PFT options:
	  --particles PARTICLES
	                        Number of particles to use for PFT. [15]
	  --back BACK_TRACKING  Length of PFT back tracking (mm). [2.0]
	  --forward FORWARD_TRACKING
	                        Length of PFT forward tracking (mm). [1.0]
	
	Output options:
	  --all                 If set, keeps "excluded" streamlines.
	                        NOT RECOMMENDED, except for debugging.
	  --seed SEED           Random number generator seed.
	  -f                    Force overwriting of the output files.
	  --save_seeds          If set, save the seeds used for the tracking 
	                         in the data_per_streamline property.
	  --compress [COMPRESS_TH]
	                        If set, compress the resulting streamline. Value is the maximum 
	                        compression distance in mm.[0.1]
	
	2.2.2