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).

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
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}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
DIPY	DIPY is the paragon 3D/4D+ imaging library in Python.	https://dipy.org	10.1016/j.neuroimage.2014.04.074
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.	https://github.com/scilus/scilpy.git

Keywords

Diffusion MRI
Tractography
Particle Filtering Tractography

Authors

@Manonedde