tracking_localtracking

process local tracking

Keywords : Tractography, Local tracking, Diffusion MRI

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Inputs

Input 1

Format : tuple val(meta), path(wm), path(fodf), path(fa)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
wm	file	Nifti image white matter probability map or mask.	True	*.{nii,nii.gz}
fodf	file	Nifti image of spherical harmonic file (fodf)	True	*.{nii,nii.gz}
fa	file	NIfti image binary mask for fa mask	True	*.{nii,nii.gz}

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Outputs

trk

Format : tuple val(meta), path(*__local_tracking.trk)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_tracking.trk	file	Tractogram output file.	True	*__local_tracking.{trk,tck}

config

Format : tuple val(meta), path(*__local_tracking_config.json)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_tracking_config.json	file	Json file containing tracking parameters.	True	*__local_tracking_config.{json}

seedmask

Format : tuple val(meta), path(*__local_seeding_mask.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_seeding_mask.nii.gz	file	Nifti seeding mask for tracking.	True	*__local_seeding_mask.{nii,nii.gz}

trackmask

Format : tuple val(meta), path(*__local_tracking_mask.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_tracking_mask.nii.gz	file	Nifti tracking mask	True	*__local_tracking_mask.{nii,nii.gz}

mqc

Format : tuple val(meta), path(*__local_tracking_mqc.png)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_tracking_mqc.png	file	PNG file containing quality control image for tracking. Made for use in MultiQC report.	True	*__local_tracking_mqc.png

global_mqc

Format : tuple val(meta), path(*__local_tracking_stats.json)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__local_tracking_stats.json	file	JSON file containing basic measurements of whole tractogram. Made for use in MultiQC report.	True	*__local_tracking_stats.json

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
local_fa_tracking_mask_threshold	float	FA threshold for the tracking mask.	0.1
local_fa_seeding_mask_threshold	float	FA threshold for the seeding mask.	0.1
local_wm_tracking_mask_threshold	float	WM threshold for the tracking mask. If the mask is binary, this threshold has no effect.	0.5
local_wm_seeding_mask_threshold	float	WM threshold for the seeding mask. If the mask is binary, this threshold has no effect.	0.5
local_tracking_mask_type	string	Strategy to use to compute the tracking mask.	wm	- wm - fa
local_seeding_mask_type	string	Strategy to use to compute the seeding mask.	wm	- wm - fa
local_step	float	Tracking Step size.	0.5
local_step_pct	float	Define the step size as a percentage of the minimum voxel dimension.	None
local_random_seed	int	Seed for random number generators.	0
local_seeding	string	Seeding strategy, either Number Per Voxel (npv) or Number Total (nt).	npv	- npv - nt
local_nbr_seeds	int	Number of seeds per voxel (if npv) or total number of seeds (if nt).	1000
local_min_len	float	Minimum length of streamlines to keep.	10.0
local_max_len	float	Maximum length of streamlines to keep.	250.0
local_theta	float	Maximum angular difference between tracking steps, in degrees.	40.0
local_sfthres	float	Spherical function threshold for tracking.	0.0
local_algo	string	Algorithm to use for tracking.	eudx	- det - prob
local_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
gpu_batch_size	int	Seed batch size for GPU processing.	10000
enable_gpu	boolean	Enable GPU tracking kernel.	False
run_qc	boolean	Enable quality control image generation for tracking.	True
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @scilus

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Last updated : 2026-05-12