ME-mppca: Building a tensor-based thermal denoising method

[marco7877]

Title

ME-mppca: Building a tensor-based thermal denoising method

Leaders

Marco Antonio Flores-Coronado @MarcoFloresCoro

Collaborators

SPiN lab (BCBL)

Brainhack Global 2024 Event

Brainhack Donostia

Project Description

• We are building a FOS library to do thermal noise reduction suited for Multi-echo acquisitions
• This will be a Python implementation of (Tensor Denoising of Multidimensional MRI Data - Olesen - 2023 - Magnetic Resonance in Medicine - Wiley Online Library). Working with python possibilitates future integration with TEDANA
• https://github.com/SPiN-Lab/ME-PCA
• Suggested reading are:
  Tensor denoising of multidimensional MRI data—Olesen—2023—Magnetic Resonance in Medicine—Wiley Online Library. (n.d.). Retrieved May 2, 2024, from https://onlinelibrary.wiley.com/doi/10.1002/mrm.29478
  Herthum, H., & Hetzer, S. (2024). Tensor denoising of quantitative multi-parameter mapping. Magnetic Resonance in Medicine, 92(1), 145–157. https://doi.org/10.1002/mrm.30050
  Veraart, J., Novikov, D. S., Christiaens, D., Ades-aron, B., Sijbers, J., & Fieremans, E. (2016). Denoising of diffusion MRI using random matrix theory. NeuroImage, 142, 394–406. https://doi.org/10.1016/j.neuroimage.2016.08.016
  original matlab implementation:
  https://github.com/Neurophysics-CFIN/MP-PCA-Denoising
  https://github.com/Neurophysics-CFIN/Tensor-MP-PCA

Link to project repository/sources

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Goals for Brainhack Global

1-Create function that takes tensor and creates a sliding window for analysis
2-Create function that performs higher-order singular value decomposition (HOSVD)
3-Documentation for library

Good first issues

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Communication channels

https://mattermost.brainhack.org/brainhack/channels/me-pca

Skills

-Python
-Knowledge or will to learn Random Matrix Theory
-Basic understanding of ME-fMRI

Onboarding documentation

No response

What will participants learn?

Matrix random theory alongside MPPCA denoising

Data to use

No response

Number of collaborators

more

Credit to collaborators

Project contributors are listed on the contributors list

Image

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Type

coding_methods, method_development

Development status

0_concept_no_content

Topic

MR_methodologies

Tools

Nipype

Programming language

Python

Modalities

fMRI

Git skills

1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[marco7877]

Hi @brainhackorg/project-monitors my project is ready!

[crnolan]

Looks good!