synthbet

Module: betcrop/synthbet

Perform brain extraction using synthstrip on image

Inputs

	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.	true	*.{nii,nii.gz}
weights	file	Alternative model weights	false	*.pt

Arguments

	Type	Description	Choices	Default
gpu	boolean	Use GPU for synthstrip		False
border	int	Mask border threshold in mm.		1
nocsf	boolean	Exclude CSF from brain border		False
model	string	Alternative model weights (see https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/ for a list of available models.		None

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bet_image	file	Nifti brain-extracted volume.	*__bet_image.{nii,nii.gz}
brain_mask	file	Brain-extracted image mask .	*__brain_mask.{nii,nii.gz}
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
Freesurfer	Software package for the analysis and visualization of structural and functional neuroimaging data.	https://surfer.nmr.mgh.harvard.edu/fswiki

Authors

@anroy1