localtracking
Module: tracking/localtracking
process local tracking
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 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 |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git |
Authors
@scilus