fslbetcrop

Module: betcrop/fslbetcrop

Perform Brain extraction using FSL BET followed by cropping empty planes around the data.

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 + crop.	true	*.{nii,nii.gz}
bval	file	B-values in FSL format.		*.bval
bvec	file	B-vectors in FSL format.	true	*.bvec

Arguments

	Type	Description	Choices	Default
b0_thr	float	Threshold under which b-values are considered to be b0s.		20
bet_f	float	Fractional intensity threshold (0->1). Smaller values give larger brain outline estimates”		0.5
size_dil	int	Size of dilation for the mask (in voxels).		None
crop	boolean	Crop the output images.		True
dilate	boolean	Dilate the mask.		True

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
image	file	Nifti volume brain-extracted and cropped.	*_bet.{nii,nii.gz}
mask	file	mask brain-extracted and cropped.	*_bet_mask.{nii,nii.gz}
bbox	file	BoundingBox used for cropping.	*_boundingBox.pkl
versions	file	File containing software versions	versions.yml

Tools

	Description	Homepage	DOI
FSL	FSL Toolbox	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.	https://github.com/scilus/scilpy.git
MRtrix3	Toolbox for image processing, analysis and visualisation of dMRI.	https://mrtrix.readthedocs.io/en/latest/

Authors

@gagnonanthony