patch-denoise 1.3.0

Denoising method for sequence of images or volumes. Primarly targeting fMRI data.

This repository implements patch-denoising methods, with a particular focus on local-low rank methods.

The target application is functional MRI thermal noise removal, but this methods can be applied to a wide range of image modalities.

It includes several local-low-rank based denoising methods:

1. MP-PCA

2. Hybrid-PCA

3. NORDIC

4. Optimal Thresholding

5. Raw Singular Value Thresholding

A mathematical description of theses methods is available in the documentation.

Installation

patch-denoise requires Python>=3.8

Quickstart

After installing you can use the patch-denoise command-line.

$ patch-denoise input_file.nii output_file.nii --mask="auto"

See patch-denoise --help for detailled options.

Documentation and Examples

Documentation and examples are available at https://paquiteau.github.io/patch-denoising/

Development version

$ git clone https://github.com/paquiteau/patch-denoising
$ pip install -e patch-denoising[dev,doc,test,optional]