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).
| 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 |
Authors
@Manonedde
