Denoise magnitude diffusion magnetic resonance images via variance-stabilizing transformation and optimal singular-value manipulation

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20 Scopus citations


Although shown to have a great utility for a wide range of neuroscientific and clinical applications, diffusion-weighted magnetic resonance imaging (dMRI) faces a major challenge of low signal-to-noise ratio (SNR), especially when pushing the spatial resolution for improved delineation of brain's fine structure or increasing the diffusion weighting for increased angular contrast or both. Here, we introduce a comprehensive denoising framework for denoising magnitude dMRI. The framework synergistically combines the variance stabilizing transform (VST) with optimal singular value manipulation. The purpose of VST is to transform the Rician data to Gaussian-like data so that an asymptotically optimal singular value manipulation strategy tailored for Gaussian data can be used. The output of the framework is the estimated underlying diffusion signal for each voxel in the image domain. The usefulness of the proposed framework for denoising magnitude dMRI is demonstrated using both simulation and real-data experiments. Our results show that the proposed denoising framework can significantly improve SNR across the entire brain, leading to substantially enhanced performances for estimating diffusion tensor related indices and for resolving crossing fibers when compared to another competing method. More encouragingly, the proposed method when used to denoise a single average of 7 ​Tesla Human Connectome Project-style diffusion acquisition provided comparable performances relative to those achievable with ten averages for resolving multiple fiber populations across the brain. As such, the proposed denoising method is expected to have a great utility for high-quality, high-resolution whole-brain dMRI, desirable for many neuroscientific and clinical applications.

Original languageEnglish (US)
Article number116852
StatePublished - Jul 15 2020

Bibliographical note

Funding Information:
The authors would like to thank Steen Moeller and Mehmet Akçakaya for their stimulating discussions on denoising, Christophe Lenglet for his valuable comments on diffusion analysis, and John Strupp and Brian Hanna for their assistance in setting up computation resources. This work was supported by NIH grants including U01 EB025144 , P41 EB015894 and P30 NS076408 .

Publisher Copyright:
© 2020 The Authors


  • Denoising
  • Diffusion MRI
  • High field MRI
  • Human connectome project
  • Simultaneous multi-slice
  • Singular value decomposition
  • Variance stabilizing transformation

Center for Magnetic Resonance Research (CMRR) tags

  • BFC
  • IRP
  • P41


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