antsbet

Module: betcrop/antsbet

Perform Brain extraction using antsBrainExtraction.sh on T1 image.

Inputs

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	true
t1	file	Nifti t1 volume to perform BET.	true	*.{nii,nii.gz}
template	file	Nifti Anatomical template to perform BET.	true	*.{nii,nii.gz}
tissues_probabilities	file	Brain probability mask (in template space), with intensity range 1 (definitely brain) to 0 (definitely background).	true	*.{nii,nii.gz}
mask	file	Brain mask (in template space) used to restrict metric computation when performing registration.	false	*.{nii,nii.gz}
initial_affine	file	Affine transform from T1w space to DWI space, used as initialization for registration algorithms.	false	*.{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

Authors

@ThoumyreStanislas