Denoising Diffusion MRI: Considerations and implications for analysis

Manzano-Patron, Jose-Pedro; Moeller, Steen; Andersson, Jesper L R; Ugurbil, Kamil; Yacoub, Essa; Sotiropoulos, Stamatios N

Abstract

Development of diffusion MRI (dMRI) denoising approaches has experienced considerable growth over the last years. As noise can inherently reduce accuracy and precision in measurements, its effects have been well characterised both in terms of uncertainty increase in dMRI-derived features and in terms of biases caused by the noise floor, the smallest measurable signal given the noise level. However, gaps in our knowledge still exist in objectively characterising dMRI denoising approaches in terms of both of these effects and assessing their efficacy. In this work, we reconsider what a denoising method should and should not do and we accordingly define criteria to characterise the performance. We propose a comprehensive set of evaluations, including i) benefits in improving signal quality and reducing noise variance, ii) gains in reducing biases and the noise floor and improving, iii) preservation of spatial resolution, iv) agreement of denoised data against a gold standard, v) gains in downstream parameter estimation (precision and accuracy), vi) efficacy in enabling noise-prone applications, such as ultra-high-resolution imaging. We further provide newly acquired complex datasets (magnitude and phase) with multiple repeats that sample different SNR regimes to highlight performance differences under different scenarios. Without loss of generality, we subsequently apply a number of exemplar patch-based denoising algorithms to these datasets, including Non-Local Means, Marchenko-Pastur PCA (MPPCA) in the magnitude and complex domain and NORDIC, and compare them with respect to the above criteria and against a gold standard complex average of multiple repeats. We demonstrate that all tested denoising approaches reduce noise-related variance, but not always biases from the elevated noise floor. They all induce a spatial resolution penalty, but its extent can vary depending on the method and the implementation. Some denoising approaches agree with the gold standard more than others and we demonstrate challenges in even defining such a standard. Overall, we show that dMRI denoising performed in the complex domain is advantageous to magnitude domain denoising with respect to all the above criteria.

Citation

Manzano-Patron, J.-P., Moeller, S., Andersson, J. L. R., Ugurbil, K., Yacoub, E., & Sotiropoulos, S. N. (2024). Denoising Diffusion MRI: Considerations and implications for analysis. Imaging Neuroscience, 2, 1-29. https://doi.org/10.1101/2023.07.24.550348

• Journal Article Type: Article
• Acceptance Date: Dec 5, 2023
• Online Publication Date: Dec 14, 2023
• Publication Date: 2024
• Deposit Date: Dec 13, 2023
• Publicly Available Date: Dec 19, 2023
• Journal: Imaging Neuroscience
• Print ISSN: 2837-6056
• Electronic ISSN: 2837-6056
• Publisher: Massachusetts Institute of Technology Press
• Peer Reviewed: Peer Reviewed
• Volume: 2
• Pages: 1-29
• DOI: https://doi.org/10.1101/2023.07.24.550348
• Keywords: Uncertainty, Noise floor, Marchenko-Pastur, DTI, Complex, MPPCA, NORDIC, NLM
• Public URL: https://nottingham-repository.worktribe.com/output/23488950
• Publisher URL: https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00060/118691/Denoising-Diffusion-MRI-Considerations-and
• Related Public URLs: https://www.biorxiv.org/content/10.1101/2023.07.24.550348v2
• Additional Information: Preprint version posted in bioRxiv on 2 Nov. 2023 at https://doi.org/10.1101/2023.07.24.550348