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Register a new userDenoising Single Voxel Magnetic Resonance Spectroscopy with Deep Learning on Repeatedly Sampled In Vivo Data
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Objective: Magnetic Resonance Spectroscopy (MRS) is a noninvasive tool to reveal metabolic information. One challenge of MRS is the relatively low Signal-Noise Ratio (SNR) due to low concentrations of metabolites. To improve the SNR, the most common approach is to average signals that are acquired in multiple times. The data acquisition time, however, is increased by multiple times accordingly, resulting in the scanned objects uncomfortable or even unbearable. Methods: By exploring the multiple sampled data, a deep learning denoising approach is proposed to learn a mapping from the low SNR signal to the high SNR one. Results: Results on simulated and in vivo data show that the proposed method significantly reduces the data acquisition time with slightly compromised metabolic accuracy. Conclusion: A deep learning denoising method was proposed to significantly shorten the time of data acquisition, while maintaining signal accuracy and reliability. Significance: Provide a solution of the fundamental low SNR problem in MRS with artificial intelligence.
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Accurate characterization of in utero human brain maturation is critical as it involves complex and interconnected structural and functional processes that may influence health later in life. Magnetic resonance imaging is a powerful tool to investigate equivocal neurological patterns during fetal development. However, the number of acquisitions of satisfactory quality available in this cohort of sensitive subjects remains scarce, thus hindering the validation of advanced image processing techniques. Numerical phantoms can mitigate these limitations by providing a controlled environment with a known ground truth. In this work, we present FaBiAN, an open-source Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates clinical T2-weighted fast spin echo sequences of the fetal brain. This unique tool is based on a general, flexible and realistic setup that includes stochastic fetal movements, thus providing images of the fetal brain throughout maturation comparable to clinical acquisitions. We demonstrate its value to evaluate the robustness and optimize the accuracy of an algorithm for super-resolution fetal brain magnetic resonance imaging from simulated motion-corrupted 2D low-resolution series as compared to a synthetic high-resolution reference volume. We also show that the images generated can complement clinical datasets to support data-intensive deep learning methods for fetal brain tissue segmentation.
A fundamental problem in X-ray Computed Tomography (CT) is the scatter due to interaction of photons with the imaged object. Unless corrected, scatter manifests itself as degradations in the reconstructions in the form of various artifacts. Scatter correction is therefore critical for reconstruction quality. Scatter correction methods can be divided into two categories: hardware-based; and software-based. Despite success in specific settings, hardware-based methods require modification in the hardware, or increase in the scan time or dose. This makes software-based methods attractive. In this context, Monte-Carlo based scatter estimation, analytical-numerical, and kernel-based methods were developed. Furthermore, data-driven approaches to tackle this problem were recently demonstrated. In this work, two novel physics-inspired deep-learning-based methods, PhILSCAT and OV-PhILSCAT, are proposed. The methods estimate and correct for the scatter in the acquired projection measurements. They incorporate both an initial reconstruction of the object of interest and the scatter-corrupted measurements related to it. They use a common deep neural network architecture and cost function, both tailored to the problem. Numerical experiments with data obtained by Monte-Carlo simulations of the imaging of phantoms reveal significant improvement over a recent purely projection-domain deep neural network scatter correction method.
Registration is the process that computes the transformation that aligns sets of data. Commonly, a registration process can be divided into four main steps: target selection, feature extraction, feature matching, and transform computation for the alignment. The accuracy of the result depends on multiple factors, the most significant are the quantity of input data, the presence of noise, outliers and occlusions, the quality of the extracted features, real-time requirements and the type of transformation, especially those ones defined by multiple parameters, like non-rigid deformations. Recent advancements in machine learning could be a turning point in these issues, particularly with the development of deep learning (DL) techniques, which are helping to improve multiple computer vision problems through an abstract understanding of the input data. In this paper, a review of deep learning-based registration methods is presented. We classify the different papers proposing a framework extracted from the traditional registration pipeline to analyse the new learning-based proposal strengths. Deep Registration Networks (DRNs) try to solve the alignment task either replacing part of the traditional pipeline with a network or fully solving the registration problem. The main conclusions extracted are, on the one hand, 1) learning-based registration techniques cannot always be clearly classified in the traditional pipeline. 2) These approaches allow more complex inputs like conceptual models as well as the traditional 3D datasets. 3) In spite of the generality of learning, the current proposals are still ad hoc solutions. Finally, 4) this is a young topic that still requires a large effort to reach general solutions able to cope with the problems that affect traditional approaches.
Magnetic resonance imaging (MRI) offers superior soft tissue contrast and is widely used in biomedicine. However, conventional MRI is not quantitative, which presents a bottleneck in image analysis and digital healthcare. Typically, additional scans are required to disentangle the effect of multiple parameters of MR and extract quantitative tissue properties. Here we investigate a data-driven strategy Q^2 MRI (Qualitative and Quantitative MRI) to derive quantitative parametric maps from standard MR images without additional data acquisition. By taking advantage of the interdependency between various MRI parametric maps buried in training data, the proposed deep learning strategy enables accurate prediction of tissue relaxation properties as well as other biophysical and biochemical characteristics from a single or a few images with conventional T_1/T_2 weighting. Superior performance has been achieved in quantitative MR imaging of the knee and liver. Q^2 MRI promises to provide a powerful tool for a variety of biomedical applications and facilitate the next generation of digital medicine.
An approach to reduce motion artifacts in Quantitative Susceptibility Mapping using deep learning is proposed. We use an affine motion model with randomly created motion profiles to simulate motion-corrupted QSM images. The simulated QSM image is paired with its motion-free reference to train a neural network using supervised learning. The trained network is tested on unseen simulated motion-corrupted QSM images, in healthy volunteers and in Parkinsons disease patients. The results show that motion artifacts, such as ringing and ghosting, were successfully suppressed.
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