localtracking
Module: tracking/localtracking
process local tracking
Keywords : Tractography, Local tracking, Diffusion MRI
Inputs
| 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. | *.{nii,nii.gz} | |
| fodf | file | Nifti image of spherical harmonic file (fodf) | *.{nii,nii.gz} | |
| fa | file | NIfti image binary mask for fa mask | *.{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} |
| seedmask | file | Nifti seeding mask for tracking. | *.{nii,nii.gz} |
| trackmask | file | Nifti tracking mask | *.{nii,nii.gz} |
| mqc | file | PNG file containing quality control image for tracking. Made for use in MultiQC report. | *local_tracking_mqc.png |
| global_mqc | file | JSON file containing basic measurements of whole tractogram. Made for use in MultiQC report. | *local_tracking_stats.json |
| versions | file | File containing software versions | versions.yml |
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_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 |
Tools
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Last updated : 2025-07-15