bundle_recognize
Extract bundles from one (or more) tractograms
Keywords : Diffusion MRI, Tractogram, Segmentation, Bundles
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(tractograms), path(transform), path(config), path(directory)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| tractograms | file | Tractogram file(s) for bundle extraction | True | *.trk |
| transform | file | Transform matrix bringing the atlas to native space | True | *.mat |
| config | file | Bundle atlas configuration file | True | *.json |
| directory | directory | Directory containing the reference atlas | True |
Outputs
Section titled “Outputs”bundles
Section titled “bundles”Format : tuple val(meta), path(*_cleaned.trk)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_cleaned.trk | file | Segmented and cleaned bundles | True | *_cleaned.trk |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| minimal_vote_ratio | float | The ratio is a value between 0 and 1. Ex: If you have 5 input model directories and a minimal_vote_ratio of 0.5, you will need at least 3 votes. | 0.5 | |
| seed | int | Seed for random number generator | 0 | |
| outlier_alpha | float | Percent of the length of the tree that clusters of individual streamlines will be pruned. | 0.6 |
| Description | DOI | |
|---|---|---|
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30