MR image reconstruction using deep density priors

Algorithms for Magnetic Resonance (MR) image reconstruction from undersampled measurements exploit prior information to compensate for missing k-space data. Deep learning (DL) provides a powerful framework for extracting such information from existing image datasets, through learning, and then using it for reconstruction. Leveraging this, recent methods employed DL to learn mappings from undersampled to fully sampled images using paired datasets, including undersampled and corresponding fully sampled images, integrating prior knowledge implicitly. In this article, we propose an alternative approach that learns the probability distribution of fully sampled MR images using unsupervised DL, specifically Variational Autoencoders (VAE), and use this as an explicit prior term in reconstruction, completely decoupling the encoding operation from the prior. The resulting reconstruction algorithm enjoys a powerful image prior to compensate for missing k-space data without requiring paired datasets for training nor being prone to associated sensitivities, such as deviations in undersampling patterns used in training and test time or coil settings. We evaluated the proposed method with T1 weighted images from a publicly available dataset, multi-coil complex images acquired from healthy volunteers (N=8) and images with white matter lesions. The proposed algorithm, using the VAE prior, produced visually high quality reconstructions and achieved low RMSE values, outperforming most of the alternative methods on the same dataset. On multi-coil complex data, the algorithm yielded accurate magnitude and phase reconstruction results. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Keywords: Reconstruction, MRI, prior probability, machine learning, deep learning, unsupervised learning, density estimationComment: Published in IEEE TMI. Main text and supplementary material, 19 pages tota

Model-based multi-parameter mapping

Quantitative MR imaging is increasingly favoured for its richer information content and standardised measures. However, computing quantitative parameter maps, such as those encoding longitudinal relaxation rate (R1), apparent transverse relaxation rate (R2*) or magnetisation-transfer saturation (MTsat), involves inverting a highly non-linear function. Many methods for deriving parameter maps assume perfect measurements and do not consider how noise is propagated through the estimation procedure, resulting in needlessly noisy maps. Instead, we propose a probabilistic generative (forward) model of the entire dataset, which is formulated and inverted to jointly recover (log) parameter maps with a well-defined probabilistic interpretation (e.g., maximum likelihood or maximum a posteriori). The second order optimisation we propose for model fitting achieves rapid and stable convergence thanks to a novel approximate Hessian. We demonstrate the utility of our flexible framework in the context of recovering more accurate maps from data acquired using the popular multi-parameter mapping protocol. We also show how to incorporate a joint total variation prior to further decrease the noise in the maps, noting that the probabilistic formulation allows the uncertainty on the recovered parameter maps to be estimated. Our implementation uses a PyTorch backend and benefits from GPU acceleration. It is available at https://github.com/balbasty/nitorch.Comment: 20 pages, 6 figures, accepted at Medical Image Analysi

Parameter optimization for local polynomial approximation based intersection confidence interval filter using genetic algorithm: an application for brain MRI image de-noising

Magnetic resonance imaging (MRI) is extensively exploited for more accuratepathological changes as well as diagnosis. Conversely, MRI suffers from variousshortcomings such as ambient noise from the environment, acquisition noise from theequipment, the presence of background tissue, breathing motion, body fat, etc.Consequently, noise reduction is critical as diverse types of the generated noise limit the efficiency of the medical image diagnosis. Local polynomial approximation basedintersection confidence interval (LPA-ICI) filter is one of the effective de-noising filters.This filter requires an adjustment of the ICI parameters for efficient window size selection.From the wide range of ICI parametric values, finding out the best set of tunes values is itselfan optimization problem. The present study proposed a novel technique for parameteroptimization of LPA-ICI filter using genetic algorithm (GA) for brain MR imagesde-noising. The experimental results proved that the proposed method outperforms theLPA-ICI method for de-noising in terms of various performance metrics for different noisevariance levels. Obtained results reports that the ICI parameter values depend on the noisevariance and the concerned under test image

Patch-based anisotropic diffusion scheme for fluorescence diffuse optical tomography-part 1: technical principles

Fluorescence diffuse optical tomography (fDOT) provides 3D images of fluorescence distributions in biological tissue, which represent molecular and cellular processes. The image reconstruction problem is highly ill-posed and requires regularisation techniques to stabilise and find meaningful solutions. Quadratic regularisation tends to either oversmooth or generate very noisy reconstructions, depending on the regularisation strength. Edge preserving methods, such as anisotropic diffusion regularisation (AD), can preserve important features in the fluorescence image and smooth out noise. However, AD has limited ability to distinguish an edge from noise. In this two-part paper, we propose a patch-based anisotropic diffusion regularisation (PAD), where regularisation strength is determined by a weighted average according to the similarity between patches around voxels within a search window, instead of a simple local neighbourhood strategy. However, this method has higher computational complexity and, hence, we wavelet compress the patches (PAD-WT) to speed it up, while simultaneously taking advantage of the denoising properties of wavelet thresholding. The proposed method combines the nonlocal means (NLM), AD and wavelet shrinkage methods, which are image processing methods. Therefore, in this first paper, we used a denoising test problem to analyse the performance of the new method. Our results show that the proposed PAD-WT method provides better results than the AD or NLM methods alone. The efficacy of the method for fDOT image reconstruction problem is evaluated in part 2

Deep learning for accelerated magnetic resonance imaging

Medical imaging has aided the biggest advance in the medical domain in the last century. Whilst X-ray, CT, PET and ultrasound are a form of imaging that can be useful in particular scenarios, they each have disadvantages in cost, image quality, ease-of-use and ionising radiation. MRI is a slow imaging protocol which contributes to its high cost to run. However, MRI is a very versatile imaging protocol allowing images of varying contrast to be easily generated whilst not requiring the use of ionising radiation. If MRI can be made to be more efficient and smart, the effective cost of running MRI may be more affordable and accessible. The focus of this thesis is decreasing the acquisition time involved in MRI whilst maintaining the quality of the generated images and thus diagnosis. In particular, we focus on data-driven deep learning approaches that aid in the image reconstruction process and streamline the diagnostic process. We focus on three particular aspects of MR acquisition. Firstly, we investigate the use of motion estimation in the cine reconstruction process. Motion allows us to combine an abundance of imaging data in a learnt reconstruction model allowing acquisitions to be sped up by up to 50 times in extreme scenarios. Secondly, we investigate the possibility of using under-acquired MR data to generate smart diagnoses in the form of automated text reports. In particular, we investigate the possibility of skipping the imaging reconstruction phase altogether at inference time and instead, directly seek to generate radiological text reports for diffusion-weighted brain images in an effort to streamline the diagnostic process. Finally, we investigate the use of probabilistic modelling for MRI reconstruction without the use of fully-acquired data. In particular, we note that acquiring fully-acquired reference images in MRI can be difficult and nonetheless may still contain undesired artefacts that lead to degradation of the dataset and thus the training process. In this chapter, we investigate the possibility of performing reconstruction without fully-acquired references and furthermore discuss the possibility of generating higher quality outputs than that of the fully-acquired references.Open Acces

Active Mean Fields for Probabilistic Image Segmentation: Connections with Chan-Vese and Rudin-Osher-Fatemi Models

Segmentation is a fundamental task for extracting semantically meaningful regions from an image. The goal of segmentation algorithms is to accurately assign object labels to each image location. However, image-noise, shortcomings of algorithms, and image ambiguities cause uncertainty in label assignment. Estimating the uncertainty in label assignment is important in multiple application domains, such as segmenting tumors from medical images for radiation treatment planning. One way to estimate these uncertainties is through the computation of posteriors of Bayesian models, which is computationally prohibitive for many practical applications. On the other hand, most computationally efficient methods fail to estimate label uncertainty. We therefore propose in this paper the Active Mean Fields (AMF) approach, a technique based on Bayesian modeling that uses a mean-field approximation to efficiently compute a segmentation and its corresponding uncertainty. Based on a variational formulation, the resulting convex model combines any label-likelihood measure with a prior on the length of the segmentation boundary. A specific implementation of that model is the Chan-Vese segmentation model (CV), in which the binary segmentation task is defined by a Gaussian likelihood and a prior regularizing the length of the segmentation boundary. Furthermore, the Euler-Lagrange equations derived from the AMF model are equivalent to those of the popular Rudin-Osher-Fatemi (ROF) model for image denoising. Solutions to the AMF model can thus be implemented by directly utilizing highly-efficient ROF solvers on log-likelihood ratio fields. We qualitatively assess the approach on synthetic data as well as on real natural and medical images. For a quantitative evaluation, we apply our approach to the icgbench dataset