Module: betcrop/synthbet
Perform brain extraction using synthstrip on image
Keywords : anatomical image, BET, freesurfer
| Type | Description | Mandatory | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| image | file | Nifti image volume to perform BET. | true | *.{nii,nii.gz} |
| weights | file | Alternative model weights | false | *.pt |
Outputs
| Type | Description | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| bet_image | file | Nifti brain-extracted volume. | *__bet_image.{nii,nii.gz} |
| brain_mask | file | Brain-extracted image mask . | *__brain_mask.{nii,nii.gz} |
| versions | file | File containing software versions | versions.yml |
| Type | Description | Default | Choices |
|---|
| gpu | boolean | Use GPU for synthstrip | False | |
| border | int | Mask border threshold in mm. | 1 | |
| nocsf | boolean | Exclude CSF from brain border | False | |
| model | string | Alternative model weights (see https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/ for a list of available models. | None | |
| Description | DOI |
|---|
| Freesurfer | Software package for the analysis and visualization of structural and functional neuroimaging data. | |
Authors
anroy1
Last updated : 2025-07-15
