segmentation_fslobes
Generate lobes parcellation using FS output
Keywords : FreeSurfer, Segmentation, Tissues
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(fs_folder)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| fs_folder | directory | FreeSurfer output folder | True |
Outputs
Section titled “Outputs”labels
Section titled “labels”Format : tuple val(meta), path(*atlas_lobes.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *atlas_lobes.nii.gz | file | Nifti lobes labels file. | True | *atlas_lobes.{nii,nii.gz} |
labels_dilate
Section titled “labels_dilate”Format : tuple val(meta), path(*atlas_lobes_dilate.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *atlas_lobes_dilate.nii.gz | file | Nifti dilated lobes labels file. | True | *atlas_lobes_dilate.{nii,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 | |
|---|---|---|---|---|
| single_thread | boolean | If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task. | False | |
| mrtrix_rng_seed | integer | Random seed for MRtrix3. Setting a fixed seed can help with reproducibility of results. | 1234 |
| Description | DOI | |
|---|---|---|
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
| MRtrix3 | Toolbox for image processing, analysis and visualisation of dMRI. |
Authors
Section titled “Authors”Last updated : 2026-05-12