utils_extractb0

Extract a b0 volume from a DWI image.

Keywords : dwi, extract, b0

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Inputs

Input 1

Format : tuple val(meta), path(dwi), path(bval), path(bvec)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
dwi	file	Nifti DWI volume to perform BET + crop.	True	*.{nii,nii.gz}
bval	file	B-values in FSL format.	True	*.bval
bvec	file	B-vectors in FSL format.	True	*.bvec

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Outputs

b0

Format : tuple val(meta), path(*_b0*.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_b0.nii.gz	file	b0 image(s) extracted from the DWI	True	*_b0*.{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
extraction_strategy	string	Extract either: all b0 (all), mean b0 (mean), mean of each continuous cluster of b0s (cluster-mean), first b0 of each continuous cluster of b0s (cluster-first).	mean	- all - mean - cluster-mean - cluster-first
b0_threshold	integer	Threshold under which b-values are considered to be b0s.	20
output_series	boolean	If output b0 volume has multiple time points, only outputs a single image instead of a numbered series of images.scil_dwi_extract_b0	False
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
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @AlexVCaron

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Last updated : 2026-04-15