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}]]
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.py 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.
Formerly: scil_compute_pft.py
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}]
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]
References: [1] Girard, G., Whittingstall K., Deriche, R., and Descoteaux, M. (2014). Towards quantitative connectivity analysis: reducing tractography biases. Neuroimage, 98, 266-278.