Denoising of volumetric magnetic resonance imaging using multi-channel three-dimensional convolutional neural network with applications on fast spin echo acquisitions.

Abstract

Three-dimensional (3D) magnetic resonance imaging (MRI) can be acquired with a high spatial resolution with flexibility being reformatted into arbitrary planes, but at the cost of reduced signal-to-noise ratio. Deep-learning methods are promising for denoising in MRI. However, the existing 3D denoising convolutional neural networks (CNNs) rely on either a multi-channel two-dimensional (2D) network or a single-channel 3D network with limited ability to extract high dimensional features. We aim to develop a deep learning approach based on multi-channel 3D convolution to utilize inherent noise information embedded in multiple number of excitation (NEX) acquisition for denoising 3D fast spin echo (FSE) MRI. A multi-channel 3D CNN is developed for denoising multi-NEX 3D FSE magnetic resonance (MR) images based on the feature extraction of 3D noise distributions embedded in 2-NEX 3D MRI. The performance of the proposed approach was compared to several state-of-the-art MRI denoising methods on both synthetic and real knee data using 2D and 3D metrics of peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM). The proposed method achieved improved denoising performance compared to the current state-of-the-art denoising methods in both slice-by-slice 2D and volumetric 3D metrics of PSNR and SSIM. A multi-channel 3D CNN is developed for denoising of multi-NEX 3D FSE MR images. The superior performance of the proposed multi-channel 3D CNN in denoising multi-NEX 3D MRI demonstrates its potential in tasks that require the extraction of high-dimensional features.