Module: betcrop/antsbet
Perform Brain extraction using antsBrainExtraction.sh on T1 image.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| t1 | file | Nifti t1 volume to perform BET. | *.{nii,nii.gz} |
| template | file | Nifti Anatomical template to perform BET. | *.{nii,nii.gz} |
| tissues_probabilities | file | Brain probability mask (in template space), with intensity range 1 (definitely brain) to 0 (definitely background). | *.{nii,nii.gz} |
| mask | file | Brain mask (in template space) used to restrict metric computation when performing registration. | *.{nii,nii.gz} |
| initial_affine | file | Affine transform from T1w space to DWI space, used as initialization for registration algorithms | *.{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 | Homepage | DOI | |
|---|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git | |
| ants | Advanced Normalization Tools. | https://github.com/ANTsX/ANTs |
Keywords
| T1 |
| BET |
| ants |
| scilpy |
Authors
@ThoumyreStanislas