pfttracking
Module: tracking/pfttracking
Compute include and exclude maps, and the seeding mask from partial volume estimation (PVE) maps. Generates a tractogram using anatomically-constrained particle filter tracking, Particle Filtering Tractography (PFT).
Keywords : Diffusion MRI, Tractography, Particle Filtering Tractography
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| wm | file | Nifti white matter probability map. | *.{nii,nii.gz} | |
| gm | file | Nifti grey matter probability map. | *.{nii,nii.gz} | |
| csf | file | Nifti cerebrospinal fuild probability map. | *.{nii,nii.gz} | |
| fodf | file | Nifti image of Spherical harmonic file (fodf). | *.{nii,nii.gz} | |
| fa | file | Nifti image of FA. | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| trk | file | Tractogram output file. | *.{trk,tck} |
| config | file | Json file containing tracking parameters. | *.{json} |
| includes | file | Nifti probability map for tracking of ending the streamline and including it in the output. | *.{nii,nii.gz} |
| excludes | file | Nifti probability map for tracking of ending the streamline and excluding it in the output. | *.{nii,nii.gz} |
| seeding | file | Nifti seeding mask for tracking. | *.{nii,nii.gz} |
| mqc | file | PNG file containing quality control image for tracking. Made for use in MultiQC report. | *pft_tracking_mqc.png |
| global_mqc | file | JSON file containing basic measurements of whole tractogram. Made for use in MultiQC report. | *pft_tracking_stats.json |
| versions | file | File containing software versions | versions.yml |
Arguments (see process.ext)
| Type | Description | Default | Choices | |
|---|---|---|---|---|
| pft_fa_seeding_mask_threshold | float | FA threshold for the seeding mask. | 0.1 | |
| pft_wm_seeding_mask_threshold | float | WM threshold for the seeding mask. | 0.5 | |
| pft_seeding_mask_type | string | Strategy to use to compute the seeding mask. | wm | wm fa |
| pft_step | float | Tracking Step size. | 0.2 | |
| pft_random_seed | int | Seed for random number generators. | 0 | |
| pft_seeding | string | Seeding strategy, either Number Per Voxel (npv) or Number Total (nt). | npv | npv nt |
| pft_nbr_seeds | int | Number of seeds per voxel (if npv) or total number of seeds (if nt). | 5 | |
| pft_min_len | float | Minimum length of streamlines to keep. | 10.0 | |
| pft_max_len | float | Maximum length of streamlines to keep. | 300.0 | |
| pft_theta | float | Maximum angular difference between tracking steps, in degrees. | 40.0 | |
| pft_sfthres | float | Spherical function threshold for tracking. | 0.1 | |
| pft_sfthres_init | float | Initial spherical function threshold for tracking. | 0.5 | |
| pft_algo | string | Algorithm to use for tracking. | prob | det prob |
| pft_compress_value | float | Compression value for the streamlines, in mm. If 0, no compression is applied. | 0.0 | |
| basis | string | Spherical basis used for FODF reconstruction. | descoteaux07_legacy | descoteaux07_legacy descoteaux07 tournier07 tournier07_legacy |
| pft_particles | int | Number of particles to use in the particle filter tracking. | 15 | |
| pft_back | float | Backtracking distance in mm. | 2.0 | |
| pft_front | float | Front tracking distance in mm. | 1.0 | |
| run_qc | boolean | Whether to run quality control (QC) on the tracking results. | True |
Tools
| Description | DOI | |
|---|---|---|
| DIPY | DIPY is the paragon 3D/4D+ imaging library in Python. | 10.1016/j.neuroimage.2014.04.074 |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Last updated : 2025-07-15