tractogram_resample
Resample bundles’ centroids.
Keywords : Bundles, Centroids, Streamlines
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(tractograms)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| tractograms | file | List of tractograms to resample. If the tractogram is a centroid file with a specific number of points, please use the nb_points parameter. | True | *.{trk} |
Outputs
Section titled “Outputs”tractograms
Section titled “tractograms”Format : tuple val(meta), path(*_resampled.trk)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| *_resampled.trk | file | Resampled tractograms. | True | *_resampled.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 | integer | Number of points per streamline in the output. | 1 | |
| nb_streamlines | integer | Number of streamlines to resample the tractogram to. | 1000 | |
| never_upsample | boolean | Make sure to never upsample a tractogram. Useful when downsampling a batch of files at once. | None | |
| seed | integer | Use a specific random seed for the resampling. | None | |
| point_wise_std | float | Noise to add to existing streamlines points to generate new ones. Value is in mm. | 1.0 | |
| tube_radius | float | Maximum distance to generate streamlines around the original ones. Value is in mm. | 1.0 | |
| gaussian | float | If set, smooth the upsampled streamlines. Value is the gaussian sigma. Uses the coordinates of surrounding points on the streamline to blur the streamlines. A good sigma choice would be around 5. | None | |
| compress | float | Compress the resulting streamline. Value is the maximum compression distance in mm. | 0.1 | |
| keep_invalid | boolean | Keep invalid newly generated streamlines that may go out of the bounding box. | False | |
| downsample_per_cluster | boolean | If set, downsampling will be done per cluster (computed with Quickbundles) to ensure that at least some streamlines are kept per bundle. Else, random downsampling is performed | False | |
| qbx_threshold | float | If you chose option ‘—downsample_per_cluster’, you may set the Quickbundles threshold value(s) here. | [40, 30, 20] |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30