MP-PCA denoising for diffusion MRS data: promises and pitfalls.

Mosso, Jessie; Simicic, Dunja; Şimşek, Kadir; Kreis, Roland; Cudalbu, Cristina; Jelescu, Ileana O (2022). MP-PCA denoising for diffusion MRS data: promises and pitfalls. NeuroImage, 263, p. 119634. Elsevier 10.1016/j.neuroimage.2022.119634

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Diffusion-weighted (DW) magnetic resonance spectroscopy (MRS) suffers from a lower signal to noise ratio (SNR) compared to conventional MRS owing to the addition of diffusion attenuation. This technique can therefore strongly benefit from noise reduction strategies. In the present work, Marchenko-Pastur principal component analysis (MP-PCA) denoising is tested on Monte Carlo simulations and on in vivo DW-MRS data acquired at 9.4T in rat brain and at 3T in human brain. We provide a descriptive study of the effects observed following different MP-PCA denoising strategies (denoising the entire matrix versus using a sliding window), in terms of apparent SNR, rank selection, noise correlation within and across b-values and quantification of metabolite concentrations and fitted diffusion coefficients. MP-PCA denoising yielded an increased apparent SNR, a more accurate B0 drift correction between shots, and similar estimates of metabolite concentrations and diffusivities compared to the raw data. No spectral residuals on individual shots were observed but correlations in the noise level across shells were introduced, an effect which was mitigated using a sliding window, but which should be carefully considered.

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