Module: betcrop/fslbetcrop
Perform Brain extraction using FSL BET followed by cropping empty planes around the data.
Keywords : DWI, T1, BET, Crop, scilpy
| 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 + crop. | true | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | | *.bval |
| bvec | file | B-vectors in FSL format. | true | *.bvec |
Outputs
| Type | Description | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| image | file | Nifti volume brain-extracted and cropped. | *_bet.{nii,nii.gz} |
| mask | file | mask brain-extracted and cropped. | *_bet_mask.{nii,nii.gz} |
| bbox | file | BoundingBox used for cropping. | *_boundingBox.pkl |
| versions | file | File containing software versions | versions.yml |
| Type | Description | Default | Choices |
|---|
| b0_thr | float | Threshold under which b-values are considered to be b0s. | 20 | |
| bet_f | float | Fractional intensity threshold (0->1). Smaller values give larger brain outline estimates” | 0.5 | |
| size_dil | int | Size of dilation for the mask (in voxels). | None | |
| crop | boolean | Crop the output images. | True | |
| dilate | boolean | Dilate the mask. | True | |
| Description | DOI |
|---|
| FSL | FSL Toolbox | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
| MRtrix3 | Toolbox for image processing, analysis and visualisation of dMRI. | |
Authors
gagnonanthony
Last updated : 2025-07-15
