fastseg
Module: segmentation/fastseg
Perform Brain Tissues Segmentation using FSL fast on a T1 image. Optionally, a binary mask of lesion can be add to correct the white matter mask.
Keywords : Segmentation, T1, Tissues
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| image | file | Nifti T1 volume to segment into tissue maps. | *.{nii,nii.gz} | |
| 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 volume. | *.{nii,nii.gz} |
| gm_mask | file | Nifti GM mask volume. | *.{nii,nii.gz} |
| csf_mask | file | Nifti CSF mask volume. | *.{nii,nii.gz} |
| wm_map | file | Nifti WM map volume. | *.{nii,nii.gz} |
| gm_map | file | Nifti GM map volume. | *.{nii,nii.gz} |
| csf_map | file | Nifti CSF map volume. | *.{nii,nii.gz} |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | DOI | |
|---|---|---|
| FSL | FSL Toolbox and Scilpy Toolbox | |
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Last updated : 2025-07-15