denoising_nlmeans

Denoise a dataset with the Non Local Means algorithm.

In order to denoise, we have three methods to estimate the noise available with their requirements:

• Sigma (needs: sigma)
• Basic sigma (needs: ncoils, optional: mask_sigma or sigma_from_all_voxels)
• Piesno (needs: ncoils)

Keywords : nifti, denoising, nlmeans, scilpy

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Inputs

Input 1

Format : tuple val(meta), path(image), path(mask), path(mask_sigma)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
image	file	Nifti image file to denoise	True	*.{nii,nii.gz}
mask	file	Nifti image file used to mask the input image	False	*.{nii,nii.gz}
mask_sigma	file	Nifti binary image file used to mask the input image for —basic_sigma estimation. Only the data inside the mask will be used to estimate sigma	False	*.{nii,nii.gz}

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Outputs

image

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

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

piesno_mask

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__piesno_mask.nii.gz	file	Piesno mask Nifti image file	True	*__piesno_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
sigma	float	Provide your own standard deviation of the noise.
basic_sigma	bool	Estimate sigma using Use dipy’s basic estimation of sigma.
piesno	bool	Estimate sigma using Piesno’s method. If data is 4D, the noise is estimated for each slice (3rd dimension).
gaussian	bool	If your data contains gaussian noise, set this option. Otherwise, Rician is assumed.
sigma_from_all_voxels	bool	If set, all voxels are used for the —basic_sigma estimation, even zeros.
save_piesno_mask	bool	If set with piesno option, it will save the piesno mask.
ncoils	int	Number of coils used for the acquisition	1

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @scilus

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Last updated : 2025-10-30