Denoising method for sequence of images or volumes. Primarly targeting fMRI data.
Project description
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 (see the documentation for more details):
MP-PCA
Hybrid-PCA
NORDIC
Optimal Thresholding
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]
Citation
If you use this package for academic work, please cite the associated publication, available on HAL
@inproceedings{comby2023, TITLE = {{Denoising of fMRI volumes using local low rank methods}}, AUTHOR = {Pierre-Antoine, Comby and Zaineb, Amor and Alexandre, Vignaud and Philippe, Ciuciu}, URL = {https://hal.science/hal-03895194}, BOOKTITLE = {{ISBI 2023 - International Symposium on Biomedical Imaging 2023}}, ADDRESS = {Carthagena de India, Colombia}, YEAR = {2023}, MONTH = Apr, KEYWORDS = {functional MRI ; patch denoising ; singular value thresholding ; functional MRI patch denoising singular value thresholding}, PDF = {https://hal.science/hal-03895194/file/isbi2023_denoise.pdf}, HAL_ID = {hal-03895194}, HAL_VERSION = {v1}, }
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file patch-denoise-1.4.2.tar.gz
.
File metadata
- Download URL: patch-denoise-1.4.2.tar.gz
- Upload date:
- Size: 40.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.5
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 174564f5fe4af7c956875dabbf197bd9354598c6059fb0538a27ae4b13496f79 |
|
MD5 | 8e8811d31e02abcf10a5a61eb36ab53f |
|
BLAKE2b-256 | 35f615c1b28c2f56a020a08d167c964938dcceb3a348da531977a322a84e5cd5 |
File details
Details for the file patch_denoise-1.4.2-py3-none-any.whl
.
File metadata
- Download URL: patch_denoise-1.4.2-py3-none-any.whl
- Upload date:
- Size: 32.7 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.5
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | aca86d83b83ecce5e329731b4cc1d243bf9e99cf8132c06ce945166536164b8b |
|
MD5 | e8b1c005f4bb6e33fe3d505fb428accb |
|
BLAKE2b-256 | f3c60e99f70c0d1540b903a78018c8d0c79ffa7a5053b6bd68f046a098c62631 |