denoising_mppca

mppca

denoise a dataset with the Marchenko-Pastur principal component analysis

Keywords : nifti, denoising, mppca

Inputs

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
dwi	file	Nifti dwi file to denoise	True	`*.{nii,nii.gz}`
mask	file	Nifti mask file for the dwi	False	`*.{nii,nii.gz}`

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

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

Format : path(versions.yml)

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

	Type	Description	Default
extent	int	Set the patch size of the denoising filter. By default, the command will select the smallest isotropic patch size that exceeds the number of DW images in the input data	“
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`
mrtrix_rng_seed	integer	Random seed for MRtrix3. Setting a fixed seed can help with reproducibility of results.	`1234`

	Description	DOI
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

Last updated : 2026-04-22