qc_tractogram
Extract a couple of QC metric based on a tractogram. - Compute DICE score between the tractogram density mask and WM mask. - Calculate the total number of streamlines from a tractogram. - Produce a QC figure showing the tractogram density image and GM mask.
Keywords : tractogram, qc, dice
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(tractogram), path(wm), path(gm)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| tractogram | file | Tractogram file in .trk format. | True | *.{trk} |
| wm | file | White matter mask in NIfTI format. | True | *.nii.gz |
| gm | file | Gray matter mask in NIfTI format. | True | *.nii.gz |
Outputs
Section titled “Outputs”tractogram_mask
Section titled “tractogram_mask”Format : tuple val(meta), path(*__tractogram_mask.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__tractogram_mask.nii.gz | file | Nifti volume - Tractogram mask. | True | *__tractogram_mask.nii.gz |
Format : tuple val(meta), path(*__TDI.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__TDI.nii.gz | file | Track Density Image (TDI) volume. | True | *__TDI.nii.gz |
Format : tuple val(meta), path(*__dice.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__dice.txt | file | Dice score between tractogram mask and white matter mask. | True | *__dice.txt |
Format : tuple val(meta), path(*__sc.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__sc.txt | file | Streamline count. | True | *__sc.txt |
Format : tuple val(meta), path(*__coverage_overlay_mqc.png)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__coverage_overlay_mqc.png | file | .png file containing quality control image for the tractogram coverage overlay. Made for use in MultiQC report. | True | *__coverage_overlay_mqc.png |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2026-03-17