Module: bundle_seg
Subworkflow to perform BundleSeg [1] to extract major white matter bundle from a tractogram.
[1] St-Onge, Etienne, Kurt G. Schilling, and Francois Rheault. “BundleSeg: A versatile,reliable and reproducible approach to white matter bundle segmentation.” International Workshop on Computational Diffusion MRI. Cham: Springer Nature Switzerland (2023)
--------- Steps -------------------- Antomical Registration (ANTs) Use the FA map from the subject to register the atlas anatomical file and compute the transformations. Bundle Recognition (scilpy) Perform bundle recognition and extraction using BundleSeg.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| ch_fa | file | The input channel containing the FA map. This map is used to compute the transformation between the atlas’ space and the subject’s space. Structure: [ val(meta), path(fa) ] | *.{nii,nii.gz} |
| ch_tractogram | file | The input channel containing the whole-brain tractogram to be segmented. Structure: [ val(meta), path(tractogram) ] | *.trk |
| atlas_directory | directory | The input channel containing the atlas directory. The folder MUST follow this specific structure: atlas_directory ├── atlas │ └── pop_average ├── centroids ├── *.json (config file) └── *.{nii,nii.gz} (atlas anatomical file) If no directory is provided, the subworkflow will automatically fetch the atlas archive available on Zenodo (https://zenodo.org/records/10103446). Structure: [ path(directory) ] |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| bundles | file | Channel containing all the segmented bundle files. Structure: [ val(meta), path(bundles) ] | *.trk |
| versions | file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
Components
| registration/ants |
| bundle/recognize |
Keywords
| BundleSeg |
| WM bundles |
| Tractogram |
| Segmentation |
Authors
@gagnonanthony
Maintainers
@gagnonanthony