bundle_bundleparc
process bundleparc
Keywords : Tractography, Bundleparc, Diffusion MRI
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(fodf), path(checkpoint)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| fodf | file | Nifti image of spherical harmonic file (fodf) - Stride -1234, with sh basis Descoteaux07 | True | *.{nii,nii.gz} |
| checkpoint | file | Checkpoint file for bundleparc | True | *.{ckpt} |
Outputs
Section titled “Outputs”labels
Section titled “labels”Format : tuple val(meta), path(*__*.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| __.nii.gz | file | Label maps | True | *.nii.gz |
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_pts | int | Number of divisions per bundle. | 10 | |
| mm | int | If set, bundles will be split in sections roughly X mm wide. | 0 | |
| continuous | bool | If set, the output label maps will be continuous ∈ [0, 1]. | False | |
| keep_biggest | bool | Only keep the biggest blob predicted. | False | |
| min_blob_size | int | Minimum blob size (in voxels) to keep. Smaller blobs will be removed. | 50 | |
| bundles | string | ”Bundles to predict, space separated. Default is every bundle (71 bundles). Check the scilpy API.” “https://scilpy.readthedocs.io/en/latest/scripts/scil_fodf_bundleparc.html” | “ | |
| half | bool | Use half precision (float16) for inference. This reduces memory usage but may lead to reduced accuracy. | False | |
| sh_basis | string | ”Spherical harmonics basis used in the input fodf. This is required to determine the number of coefficients per voxel.” “Only ‘descoteaux07’ is currently supported. but needs to be specified for the module to run.” ” You need to link this parameter with params.fodf_sh_basis from tractoflow subworkflow and/or params.sh_basis from fodf module” | “ |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2026-05-12