bundle_labelmap
Compute the label image (Nifti) from a centroid and tractograms (all representing the same bundle). The label image represents the coverage of the bundle, segmented into regions labelled from 0 to —nb_pts, starting from the head, ending in the tail. Each voxel will have the label of its nearest centroid point. The number of labels will be the same as the centroid’s number of points.
Keywords : bundle, distance, label, centroid
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(bundles), path(centroids)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| bundles | file | List of trk files of the bundles | True | *.{trk} |
| centroids | file | List of trk files of the centroids | True | *.{trk} |
Outputs
Section titled “Outputs”labels
Section titled “labels”Format : tuple val(meta), path(*_labels.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_labels.nii.gz | file | Labels map, each pixel intensity corresponds to the label of the nearest centroid. | True | *_labels.nii.gz |
labels_trk
Section titled “labels_trk”Format : tuple val(meta), path(*_labels.trk)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_labels.trk | file | Colored by labels bundle file. The streamline color corresponds to the label of the nearest centroid. | True | *_labels.trk |
distances
Section titled “distances”Format : tuple val(meta), path(*_distances.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_distances.nii.gz | file | Distance map. The pixel intensity corresponds to the distance to the nearest centroid. | True | *_distances.nii.gz |
distances_trk
Section titled “distances_trk”Format : tuple val(meta), path(*_distances.trk)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_distances.trk | file | Colored by distance bundle file. The streamline color corresponds to the distance to the nearest centroid. | True | *_distances.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 | |
|---|---|---|---|---|
| nb_points | int | Number of divisions for the bundles. | Number of points of the centroid | |
| colormap | string | Select the colormap for colored trk (data_per_point). | jet | |
| threshold | float | Maximum distance between two points to be considered overlapping. | 0.001 | |
| streamline_threshold | float | Threshold for the minimum number of streamlines in a voxel to be included. | 2 | |
| use_hyperplane | boolean | Use hyperplane method (multi-centroids) instead of the euclidean method (single-centroid). | False | |
| use_manhattan | boolean | Use the Manhattan distance instead of the Euclidean distance. | False | |
| skip_uniformize | boolean | Skip the uniformization of the bundles orientation. | False | |
| correlation_threshold | float | Threshold for the correlation map. Only for the multi-bundle case. | 0.0 |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-12-22