betcrop_synthstrip

Perform brain extraction using synthstrip on image

Keywords : anatomical image, BET, synthetic, neural network, Artificial intelligence, machine learning

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Inputs

Input 1

Format : tuple val(meta), path(image), path(weights)

	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

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Outputs

bet_image

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

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

brain_mask

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__brain_mask.nii.gz	file	Brain-extracted image mask .	True	*__brain_mask.{nii,nii.gz}

versions

Format : path(versions.yml)

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

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Arguments (see process.ext)

	Type	Description	Default	Choices
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
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False

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Tools

	Description	DOI
Freesurfer	Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.	10.1016/j.neuroimage.2012.01.021

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Authors

• @anroy1

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Last updated : 2026-04-23