Enhancing the estimation of fiber orientation distributions using convolutional neural networks. (August 2021)

• Record Type: Journal Article
• Authors: Lucena, Oeslle; Vos, Sjoerd B.; Vakharia, Vejay; Duncan, John; Ashkan, Keyoumars; Sparks, Rachel; Ourselin, Sebastien
• Is Part Of: Computers in biology and medicine. Volume 135(2021)
• Publication Date: 2021-08
• Subjects: Diffusion weighted image -- Deep learning -- Constrained spherical deconvolution -- Tractography; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2021.104643
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: Local fiber orientation distributions (FODs) can be computed from diffusion magnetic resonance imaging (dMRI). The accuracy and ability of FODs to resolve complex fiber configurations benefits from acquisition protocols that sample a high number of gradient directions, a high maximum b-value, and multiple b-values. However, acquisition time and scanners that follow these standards are limited in clinical settings, often resulting in dMRI acquired at a single shell (single b-value). In this work, we learn improved FODs from clinically acquired dMRI. We evaluate patch-based 3D convolutional neural networks (CNNs) on their ability to regress multi-shell FODs from single-shell FODs, using constrained spherical deconvolution (CSD). We evaluate U-Net and High-Resolution Network (HighResNet) 3D CNN architectures on data from the Human Connectome Project and an in-house dataset. We evaluate how well each CNN can resolve FODs 1) when training and testing on datasets with the same dMRI acquisition protocol; 2) when testing on a dataset with a different dMRI acquisition protocol than used to train the CNN; and 3) when testing on a dataset with a fewer number of gradient directions than used to train the CNN. This work is a step towards more accurate FOD estimation in time- and resource-limited clinical environments. Highlights: Improved estimation of fiber orientations distributions (FODs) for clinically acquired singleshell diffusion MRI (dMRI). Evaluation of how well CNNs can resolve FODs for dMRI with the same and for different acquisition protocols. A step towards more accurate FOD estimation in time- and resource-limited clinical environments.