Module: betcrop/fslbetcrop
Perform Brain extraction using FSL BET followed by cropping empty planes around the data.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| image | file | Nifti image volume to perform BET + crop. | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | *.bval |
| bvec | file | B-vectors in FSL format. | *.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 |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| FSL | FSL Toolbox | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git | |
| MRtrix3 | Toolbox for image processing, analysis and visualisation of dMRI. | https://mrtrix.readthedocs.io/en/latest/ |
Keywords
| DWI |
| T1 |
| BET |
| Crop |
| scilpy |
Authors
@gagnonanthony