preproc_normalize

Normalize DWI using MRtrix3 (in WM)

Keywords : nifti, normalise, scilpy

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Inputs

Input 1

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
dwi	file	Nifti image file to normalize	True	*.{nii,nii.gz}
bval	file	Text file containing b-values	True	*.{.bval}
bvec	file	Text file containing b-vectors	True	*.{.bvec}
mask	file	Nifti image file used to mask the input image	True	*.{nii,nii.gz}

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Outputs

dwi

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*dwi_normalized.nii.gz	file	Normalized Nifti image file	True	*dwi_normalized.{nii,nii.gz}

mask

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*fa_wm_mask.nii.gz	file	Nifti image file mask	True	*fa_wm_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
dwi_shell_tolerance	integer	Tolerance in s/mm2 for grouping b-values into shells. E.g. with a tolerance of 20, b-values between 0 and 20 will be considered as b=0.	None
fa_mask_threshold	float	Threshold to apply on the FA map to create a white matter mask.	None
max_dti_shell_value	integer	Maximum b-value to use for DTI fitting. All shells under this value will be used.
dti_shells	string	Space separated list of b-values to use for DTI fitting. If None, all shells under max_dti_shell_value will be used.	None

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
MRtrix3	MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging.	10.1016/j.neuroimage.2019.116137

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Authors

• @scilus

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Last updated : 2025-10-30