antsbet
Module: betcrop/antsbet
Perform Brain extraction using antsBrainExtraction.sh on T1 image.
Keywords : T1, BET, ants, scilpy
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| t1 | file | Nifti t1 volume to perform BET. | true | *.{nii,nii.gz} |
| template | file | Nifti Anatomical template to perform BET. | true | *.{nii,nii.gz} |
| tissues_probabilities | file | Brain probability mask (in template space), with intensity range 1 (definitely brain) to 0 (definitely background). | true | *.{nii,nii.gz} |
| mask | file | Brain mask (in template space) used to restrict metric computation when performing registration. | false | *.{nii,nii.gz} |
| initial_affine | file | Affine transform from T1w space to DWI space, used as initialization for registration algorithms. | false | *.{mat/txt} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| t1 | file | Nifti T1 volume brain-extracted. | *t1_bet.{nii,nii.gz} |
| mask | file | T1 mask brain-extracted and cropped. | *t1_bet_mask.{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. | |
| ants | Advanced Normalization Tools. |
Authors
Last updated : 2025-07-15