betcrop_fslbetcrop
Perform Brain extraction using FSL BET followed by cropping empty planes around the data.
Keywords : DWI, T1, BET, Crop
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(image), path(bval), path(bvec)
| 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. | True | *.bval |
| bvec | file | B-vectors in FSL format. | True | *.bvec |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*_bet.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_bet.nii.gz | file | Nifti volume brain-extracted and cropped. | True | *_bet.{nii,nii.gz} |
Format : tuple val(meta), path(*_bet_mask.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_bet_mask.nii.gz | file | mask brain-extracted and cropped. | True | *_bet_mask.{nii,nii.gz} |
Format : tuple val(meta), path(*_boundingBox.pkl)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_boundingBox.pkl | file | BoundingBox used for cropping. | True | *_boundingBox.pkl |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| 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 | 10.1016/j.neuroimage.2011.09.015 |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
| MRtrix3 | MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging. | 10.1016/j.neuroimage.2019.116137 |
Authors
Section titled “Authors”Last updated : 2025-10-30