Magnetic Resonance Spectroscopy Quantification Aided by Deep Estimations of Imperfection Factors and Macromolecular Signal.

OBJECTIVE: Magnetic Resonance Spectroscopy (MRS) is an important technique for biomedical detection. However, it is challenging to accurately quantify metabolites with proton MRS due to serious overlaps of metabolite signals, imperfections because of non-ideal acquisition conditions, and interference with strong background signals mainly from macromolecules. The most popular method, LCModel, adopts complicated non-linear least square to quantify metabolites and addresses these problems by designing empirical priors such as basis-sets, imperfection factors. However, when the signal-to-noise ratio of MRS signal is low, the solution may have large deviation. METHODS: Linear Least Squares (LLS) is integrated with deep learning to reduce the complexity of solving this overall quantification. First, a neural network is designed to explicitly predict the imperfection factors and the overall signal from macromolecules. Then, metabolite quantification is solved analytically with the introduced LLS. In our Quantification Network (QNet), LLS takes part in the backpropagation of network training, which allows the feedback of the quantification error into metabolite spectrum estimation. This scheme greatly improves the generalization to metabolite concentrations unseen in training compared to the end-to-end deep learning method. RESULTS: Experiments show that compared with LCModel, the proposed QNet, has smaller quantification errors for simulated data, and presents more stable quantification for 20 healthy in vivo data at a wide range of signal-to-noise ratio. QNet also outperforms other end-to-end deep learning methods. CONCLUSION: This study provides an intelligent, reliable and robust MRS quantification. SIGNIFICANCE: QNet is the first LLS quantification aided by deep learning.

CloudBrain-MRS: An intelligent cloud computing platform for in vivo magnetic resonance spectroscopy preprocessing, quantification, and analysis.

Magnetic resonance spectroscopy (MRS) is an important clinical imaging method for diagnosis of diseases. MRS spectrum is used to observe the signal intensity of metabolites or further infer their concentrations. Although the magnetic resonance vendors commonly provide basic functions of spectrum plots and metabolite quantification, the spread of clinical research of MRS is still limited due to the lack of easy-to-use processing software or platform. To address this issue, we have developed CloudBrain-MRS, a cloud-based online platform that provides powerful hardware and advanced algorithms. The platform can be accessed simply through a web browser, without the need of any program installation on the user side. CloudBrain-MRS also integrates the classic LCModel and advanced artificial intelligence algorithms and supports batch preprocessing, quantification, and analysis of MRS data from different vendors. Additionally, the platform offers useful functions: (1) Automatically statistical analysis to find biomarkers for diseases; (2) Consistency verification between the classic and artificial intelligence quantification algorithms; (3) Colorful three-dimensional visualization for easy observation of individual metabolite spectrum. Last, data of both healthy subjects and patients with mild cognitive impairment are used to demonstrate the functions of the platform. To the best of our knowledge, this is the first cloud computing platform for in vivo MRS with artificial intelligence processing. We have shared our cloud platform at MRSHub, providing at least two years of free access and service. If you are interested, please visit https://mrshub.org/software_all/#CloudBrain-MRS or https://csrc.xmu.edu.cn/CloudBrain.html.

Spatiotemporal Flexible Sparse Reconstruction for Rapid Dynamic Contrast-Enhanced MRI.

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a tissue perfusion imaging technique. Some versatile free-breathing DCE-MRI techniques combining compressed sensing (CS) and parallel imaging with golden-angle radial sampling have been developed to improve motion robustness with high spatial and temporal resolution. These methods have demonstrated good diagnostic performance in clinical setting, but the reconstruction quality will degrade at high acceleration rates and overall reconstruction time remains long. In this paper, we proposed a new parallel CS reconstruction model for DCE-MRI that enforces flexible weighted sparse constraint along both spatial and temporal dimensions. Weights were introduced to flexibly adjust the importance of time and space sparsity, and we derived a fast-thresholding algorithm which was proven to be simple and efficient for solving the proposed reconstruction model. Results on both the brain tumor DCE and liver DCE show that, at relatively high acceleration factor of fast sampling, lowest reconstruction error and highest image structural similarity are obtained by the proposed method. Besides, the proposed method achieves faster reconstruction for liver datasets and better physiological measures are also obtained on tumor images.

Brain metabolic differences between temporal lobe epileptic seizures and organic non-epileptic seizures in postictal phase: a retrospective study with magnetic resonance spectroscopy.

Magnetic resonance spectroscopy (MRS) is employed to investigate the brain metabolites differences between patients with temporal lobe epileptic seizures (TLES) and organic non-epileptic seizures (ONES) that appear to be epileptic seizures. Twenty-three patients with TLES and nine patients with ONES in postictal phase underwent MRS examinations on a clinical 1.5T system, with 15 healthy controls in comparison. Statistical analyses on the ratios of brain metabolites were performed using the Mann-Whitney U test with age as a covariate. The results showed that N-acetyl-aspartate/Creatine (NAA/Cr) ratio of patients with TLES was statistically different from that of patients with ONES in postictal phase, i.e., TLES 1.422±0.037, ONES 1.640±0.061, P=0.012 in left temporal pole, while TLES 1.470±0.052, ONES 1.687±0.084, P=0.023 in the right temporal pole. Besides, compared with healthy controls, patients with TLES in postictal phase present significant differences in ratios of NAA/Cr, N-acetyl-aspartate/Choline (NAA/Cho) and NAA/(Cho + Cr). Experimental results demonstrate that NAA/Cr can be used to discriminate TLES from ONES, which has not been found in the references to the best of our knowledge. Although a prospective controlled validation is needed in the future, this retrospective study reveals that MRS may provide useful metabolites information to facilitate the epilepsy diagnosis.

Coil Combination of Multichannel Single Voxel Magnetic Resonance Spectroscopy with Repeatedly Sampled In Vivo Data.

Magnetic resonance spectroscopy (MRS), as a noninvasive method for molecular structure determination and metabolite detection, has grown into a significant tool in clinical applications. However, the relatively low signal-to-noise ratio (SNR) limits its further development. Although the multichannel coil and repeated sampling are commonly used to alleviate this problem, there is still potential room for promotion. One possible improvement way is combining these two acquisition methods so that the complementary of them can be well utilized. In this paper, a novel coil-combination method, average smoothing singular value decomposition, is proposed to further improve the SNR by introducing repeatedly sampled signals into multichannel coil combination. Specifically, the sensitivity matrix of each sampling was pretreated by whitened singular value decomposition (WSVD), then the smoothing was performed along the repeated samplings' dimension. By comparing with three existing popular methods, Brown, WSVD, and generalized least squares, the proposed method showed better performance in one phantom and 20 in vivo spectra.

Review and Prospect: Deep Learning in Nuclear Magnetic Resonance Spectroscopy.

Since the concept of deep learning (DL) was formally proposed in 2006, it has had a major impact on academic research and industry. Nowadays, DL provides an unprecedented way to analyze and process data with demonstrated great results in computer vision, medical imaging, natural language processing, and so forth. Herein, applications of DL in NMR spectroscopy are summarized, and a perspective for DL as an entirely new approach that is likely to transform NMR spectroscopy into a much more efficient and powerful technique in chemistry and life sciences is outlined.