Denoising single MR spectra by deep learning: Miracle or mirage?

Magn Reson Med. 2023 Nov;90(5):1749-1761. doi: 10.1002/mrm.29762. Epub 2023 Jun 18.


Purpose: The inherently poor SNR of MRS measurements presents a significant hurdle to its clinical application. Denoising by machine or deep learning (DL) was proposed as a remedy. It is investigated whether such denoising leads to lower estimate uncertainties or whether it essentially reduces noise in signal-free areas only.

Methods: Noise removal based on supervised DL with U-nets was implemented using simulated 1 H MR spectra of human brain in two approaches: (1) via time-frequency domain spectrograms and (2) using 1D spectra as input. Quality of denoising was evaluated in three ways: (1) by an adapted fit quality score, (2) by traditional model fitting, and (3) by quantification via neural networks.

Results: Visually appealing spectra were obtained; hinting that denoising is well-suited for MRS. However, an adapted denoising score showed that noise removal is inhomogeneous and more efficient for signal-free areas. This was confirmed by quantitative analysis of traditional fit results as well as DL quantitation following DL denoising. DL denoising, although apparently successful as judged by mean squared errors, led to substantially biased estimates in both implementations.

Conclusion: The implemented DL-based denoising techniques may be useful for display purposes, but do not help quantitative evaluations, confirming expectations based on estimation theory: Cramér Rao lower bounds defined by the original data and the appropriate fitting model cannot be circumvented in an unbiased way for single data sets, unless additional prior knowledge can be incurred in the form of parameter restrictions/relations or applicable substates.

Keywords: MR spectroscopy; deep learning; denoising; machine learning; parameter estimation; quantification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brain / diagnostic imaging
  • Deep Learning*
  • Humans
  • Image Processing, Computer-Assisted / methods
  • Neural Networks, Computer
  • Signal-To-Noise Ratio