bundle_seg
bundle_seg
Section titled “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 --------------------
- Anatomical 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.
--------- Experimental features -----
DISCLAIMER !!! The following features are experimental and may not work as expected. While we run tests to ensure computational stability of the subworkflow, we cannot guarantee the correctness of the results.
Anatomical Registration (SynthMorph) : params.run_synthmorph = true Synthmorph is a machine learning-based registration method developed by the Freesurfer team. It is made available in this subworkflow by the REGISTRATION subworkflow, please refer to its documentation for more details.
Keywords : BundleSeg, WM bundles, Tractogram, Segmentation
Components : bundle/recognize, registration
Inputs
Section titled “Inputs”| Type | Description | Mandatory | 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) ] | True | *.{nii,nii.gz} |
| ch_tractogram | file | The input channel containing the whole-brain tractogram to be segmented. Structure: [ val(meta), path(tractogram) ] | True | *.trk |
| ch_freesurfer_license | file | ONLY USED WITH SYNTHMORPH REGISTRATION. The input channel containing the Freesurfer license file. Structure: [ val(meta), path(license) ] | False | *.txt |
Outputs
Section titled “Outputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| bundles | file | Channel containing all the segmented bundle files. Structure: [ val(meta), path(bundles) ] | True | *.trk |
| mqc | file | Channel containing QC data for MultiQC reports. Structure: [ *mqc.* ] | False | *mqc.* |
| bundles_mqc | file | Channel containing the bundle segmentation mosaic images for QC. Structure: [ *_bundles_mosaic_mqc.png ] | False | *_bundles_mosaic_mqc.png |
| stats_mqc | file | Channel containing the bundle segmentation statistics for QC. Structure: [ *_bundles_stats_mqc.json ] | False | *_bundles_stats_mqc.json |
| versions | file | File containing software versions Structure: [ path(versions.yml) ] | True | versions.yml |
Parameters (see configuration)
Section titled “Parameters (see configuration)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| run_synthmorph | boolean | Run SynthMorph registration instead of ANTs. | False | |
| atlas_directory | directory | Use an alternative atlas to the default BundleSeg one available on Zenodo (https://zenodo.org/records/10103446). The folder MUST follow the same organisation as archive atlas.zip hosted on Zenodo at the link above. |
Authors
Section titled “Authors”Maintainers
Section titled “Maintainers”Last updated : 2025-12-22