DWI_Denoise

Denoising of the DWI with DIPY (MP-PCA or Patch2Self). Use it first in the pipeline, on the raw images, before any interpolation and before GIBBS_Correct

Command:

dmriprep

Module version:

0.1

Module type:

prep

Attributes:

deform_image

Notes:

DWI_Denoise README

Source:

dtiplayground/dmri/preprocessing/modules/DWI_Denoise

Protocol options

method

Denoising method

Type:

list

Default:

mppca

Choices:

• mppca – Marchenko-Pastur PCA of local patches (Veraart et al. 2016), the method of MRtrix dwidenoise. Also writes the noise level map (DWI_noise_sigma)

• patch2self – Self-supervised denoising, each volume predicted from the other volumes (Fadnavis et al. 2020); b-values up to 50 are the b=0 volumes (as in QSIPrep). Also writes the RMS of the removed signal (DWI_noise_residual)

patchRadius

Radius of the patches of MP-PCA in voxels (2 is a 5x5x5 patch). 0 chooses the smallest patch with at least as many voxels as there are volumes

Type:

integer

Default:

0

patch2selfModel

Regression model of Patch2Self

Type:

list

Default:

ols

Choices:

• ols – Ordinary least squares

• ridge – Ridge regression

• lasso – Lasso regression