betcrop_antsbet

Perform Brain extraction using antsBrainExtraction.sh on T1 image.

Keywords : T1, mask, brain, extraction

Inputs

Format : tuple val(meta), path(t1), path(template), path(tissues_probabilities), path(mask), path(initial_affine)

	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}`

Format : tuple val(meta), path(*t1_bet.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*t1_bet.nii.gz	file	Nifti T1 volume brain-extracted.	True	`*t1_bet.{nii,nii.gz}`

Format : tuple val(meta), path(*t1_bet_mask.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*t1_bet_mask.nii.gz	file	T1 mask brain-extracted and cropped.	True	`*t1_bet_mask.{nii,nii.gz}`

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	`versions.yml`

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
ANTs	Advanced Normalization Tools (ANTs) for image processing.	10.1038/s41598-021-87564-6

Last updated : 2025-10-30