An improved deep network for tissue microstructure estimation with uncertainty quantification

• Published in: Medical image analysis Vol. 61; p. 101650
• Main Authors: Ye, Chuyang, Li, Yuxing, Zeng, Xiangzhu
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2020
• Subjects: Connectome; Deep Learning; Deep network; Diffusion Magnetic Resonance Imaging; Humans; Image Enhancement - methods; Separable dictionary; Tissue microstructure; Uncertainty; Uncertainty quantification; White Matter - ultrastructure; Uncertainty quantification; Deep network; Separable dictionary; Tissue microstructure
• ISSN: 1361-8415; 1361-8423
• DOI: 10.1016/j.media.2020.101650

•We have proposed an improved deep network for tissue microstructure estimation.•We exploit signal sparsity in the spatial-angular domain with a separable dictionary.•Quantification of estimation uncertainty is also developed using Lasso bootstrap.•The proposed method outperforms competing methods in terms of estimation accuracy.•The proposed method also produces reasonable uncertainty quantification results. [Display omitted] Deep learning based methods have improved the estimation of tissue microstructure from diffusion magnetic resonance imaging (dMRI) scans acquired with a reduced number of diffusion gradients. These methods learn the mapping from diffusion signals in a voxel or patch to tissue microstructure measures. In particular, it is beneficial to exploit the sparsity of diffusion signals jointly in the spatial and angular domains, and the deep network can be designed by unfolding iterative processes that adaptively incorporate historical information for sparse reconstruction. However, the number of network parameters is huge in such a network design, which could increase the difficulty of network training and limit the estimation performance. In addition, existing deep learning based approaches to tissue microstructure estimation do not provide the important information about the uncertainty of estimates. In this work, we continue the exploration of tissue microstructure estimation using a deep network and seek to address these limitations. First, we explore the sparse representation of diffusion signals with a separable spatial-angular dictionary and design an improved deep network for tissue microstructure estimation. The procedure for updating the sparse code associated with the separable dictionary is derived and unfolded to construct the deep network. Second, with the formulation of sparse representation of diffusion signals, we propose to quantify the uncertainty of network outputs with a residual bootstrap strategy. Specifically, because of the sparsity constraint in the signal representation, we perform a Lasso bootstrap strategy for uncertainty quantification. Experiments were performed on brain dMRI scans with a reduced number of diffusion gradients, where the proposed method was applied to two representative biophysical models for describing tissue microstructure and compared with state-of-the-art methods of tissue microstructure estimation. The results show that our approach compares favorably with the competing methods in terms of estimation accuracy. In addition, the uncertainty measures provided by our method correlate with estimation errors and produce reasonable confidence intervals; these results suggest potential application of the proposed uncertainty quantification method in brain studies.