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Supervised denoising of diffusion-weighted magnetic resonance images using a convolutional neural network and transfer learning

Jurek Jakub, Materka Andrzej, Ludwisiak Kamil, Majos Agata, Gorczewski Kamil, Cepuch Kamil, Zawadzka Agata

Biocybernetics and Biomedical Engineering

2023

Vol. 43, no. 1

206--232

In this paper, we propose a method for reducing thermal noise in diffusion-weighted magnetic resonance images (DWI MRI) of the brain using a convolutional neural network (CNN) trained on realistic, synthetic MR data. Two reference methods are considered: a) averaging of repeated scans, a widespread method used in clinics to improve signal-to-noise ratio of MR images and b) the blockwise Non-Local Means (NLM) filter, one of the post-processing methods frequently used in DWI denoising. To obtain training data for transfer learning, the effects of echo-planar imaging (EPI) – Nyquist ghosting and ramp sampling – are modelled in a data-driven fashion. These effects are introduced to the digital phantom of brain anatomy (BrainWeb). Real noise maps are obtained from the MRI scanner with a brainDWI-designed protocol and later combined with simulated, noise-free EPI images. The Point Spread Function is measured in a DW image of an AJR-approved geometrical phantom. Inter-scan patient movement is captured from a brain scan of a healthy volunteer using image registration. The denoising methods are applied to the simulated EPI brain images and in real EPI DWI of the brain. The quality of denoised images is evaluated at several signal-to-noise ratios. The characteristics of noise residuals are studied thoroughly. A diffusion phantom is used to investigate the influence of denoising on ADC measurements. The method is also evaluated on a GRAPPA dataset. We show that our method outperforms NLM and image averaging and allows for a significant reduction in scan time by lowering the number of repeated scans. We also analyse the trained CNN denoisers and point out the challenges accompanying this denoising method.

CNN-based superresolution reconstruction of 3D MR images using thick-slice scans

Jurek Jakub, Kocinski Marek, Materka Andrzej, Elgalal Marcin, Majos Agata

Biocybernetics and Biomedical Engineering

2020

Vol. 40, no. 1

111--125

Due to inherent physical and hardware limitations, 3D MR images are often acquired in the form of orthogonal thick slices, resulting in highly anisotropic voxels. This causes the partial volume effect, which introduces blurring of image details, appearance of staircase artifacts and significantly decreases the diagnostic value of images. To restore high resolution isotropic volumes, we propose to use a convolutional neural network (CNN) driven by patches taken from three orthogonal thick-slice images. To assess the validity and efficiency of this postprocessing approach, we used 1x1x1 mm3-voxel brain images of different modalities, available via the well known BrainWeb database. They served as a high resolution reference and were numerically preprocessed to create input images of different slice thickness and anatomical orientation, for CNN training, validation and testing. The visual quality of reconstructed images was indeed superior, compared to images obtained by fusion of interpolated thick-slice images, or to images reconstructed with the CNN using a single input MR scan. The significant increase of objectively computed figures of merit, e.g. the Structural Similarity Image Metric, was also noticed. Keeping in mind that any single value of such quality metrics represents a number of psychophysical effects, we applied the CNN trained on brain images for superresolution reconstruction of synthetic and acquired blood vessel tree images. We then used the restored superresolution volumes for estimation of vessel radii. It was demonstrated that vessel radius values derived from superresolution images of simulated vessel trees are significantly more accurate than those obtained from a standard fusion of interpolated thick-slice orthogonal scans. Superiority of the CNN-based superresolution images was also observed for scanner-acquired MR scans according to the evaluated parameters. These three experiments show the efficiency of CNN-based image reconstruction for qualitative and quantitative improvement of its diagnostic quality, as well as illustrates the practical usefulness of transfer learning - networks trained on example images of one kind can be used to restore superresolution images of physically different objects.