freesurferseg
Module: segmentation/freesurferseg
Performs Brain Tissues Segmentation using the FreeSurfer aparc and wmparc output files. Optionally, a binary mask of lesion can be add to correct the white matter mask.
Keywords : FreeSurfer, Segmentation, Tissues
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| aparc_aseg | file | FreeSurfer cortical and subcortical parcellation output file. | *.mgz | |
| wmparc | file | FreeSurfer WM parcellation output file. | *.mgz | |
| lesion | file | Nifti lesion volume to correct the white matter with a lesion mask. The lesion mask must be a binary mask. | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| wm_mask | file | Nifti WM mask file. | *.{nii,nii.gz} |
| gm_mask | file | Nifti GM mask file. | *.{nii,nii.gz} |
| csf_mask | file | Nifti CSF mask file. | *.{nii,nii.gz} |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | DOI | |
|---|---|---|
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
| MRtrix3 | Toolbox for image processing, analysis and visualisation of dMRI. |
Authors
Last updated : 2025-07-15