Deep learning has shown great promise for MRI reconstruction from undersampled data, yet there is a lack of research on validating its performance in 3D parallel imaging acquisitions with non-Cartesian undersampling. In addition, the artifacts and the resulting image quality depend on the under-sampling pattern. To address this uncharted territory, we extend the Non-Cartesian Primal-Dual Network (NC-PDNet), a state-of-the-art unrolled neural network, to a 3D multi-coil setting. We evaluated the impact of channel-specific versus channel-agnostic training configurations and examined the effect of coil compression. Finally, we benchmark four distinct non-Cartesian undersampling patterns, with an acceleration factor of six, using the publicly available Calgary-Campinas dataset. Our results show that NC-PDNet trained on compressed data with varying input channel numbers achieves an average PSNR of 42.98 dB for 1 mm isotropic 32 channel whole-brain 3D reconstruction. With an inference time of 4.95sec and a GPU memory usage of 5.49 GB, our approach demonstrates significant potential for clinical research application.
University of Amsterdam（阿姆斯特丹大学）；Facebook AI Research（Facebook人工智能研究院）
Most current approaches to undersampled multi-coil MRI reconstruction focus on learning the reconstruction model for a fixed, equidistant acquisition trajectory. In this paper, we study the problem of joint learning of the reconstruction model together with acquisition policies. To this end, we extend the End-to-End Variational Network with learnable acquisition policies that can adapt to different data points. We validate our model on a coil-compressed version of the large scale undersampled multi-coil fastMRI dataset using two undersampling factors: $4\times$ and $8\times$. Our experiments s…
Nanchang University（南昌大学）；Paul C. Lauterbur Research Center for Biomedical Imaging, SIAT, CAS（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）
The integration of compressed sensing and parallel imaging (CS-PI) provides a robust mechanism for accelerating MRI acquisitions. However, most such strategies require the explicit formation of either coil sensitivity profiles or a cross-coil correlation operator, and as a result reconstruction corresponds to solving a challenging bilinear optimization problem. In this work, we present an unsupervised deep learning framework for calibration-free parallel MRI, coined universal generative modeling for parallel imaging (UGM-PI). More precisely, we make use of the merits of both wavelet transform …
University of Florida（佛罗里达大学）；Georgia State University（佐治亚州立大学）
We propose a novel deep neural network architecture by mapping the robust proximal gradient scheme for fast image reconstruction in parallel MRI (pMRI) with regularization function trained from data. The proposed network learns to adaptively combine the multi-coil images from incomplete pMRI data into a single image with homogeneous contrast, which is then passed to a nonlinear encoder to efficiently extract sparse features of the image. Unlike most of existing deep image reconstruction networks, our network does not require knowledge of sensitivity maps, which can be difficult to estimate acc…
Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）；Research Center for Medical AI, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院医学人工智能研究中心）；Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences（中国科学院大学深圳先进技术学院）；The State University of New York, Buffalo（纽约州立大学布法罗分校）
Deep learning has achieved good success in cardiac magnetic resonance imaging (MRI) reconstruction, in which convolutional neural networks (CNNs) learn a mapping from the undersampled k-space to the fully sampled images. Although these deep learning methods can improve the reconstruction quality compared with iterative methods without requiring complex parameter selection or lengthy reconstruction time, the following issues still need to be addressed: 1) all these methods are based on big data and require a large amount of fully sampled MRI data, which is always difficult to obtain for cardiac…
We convert the information-rich measurements of parallel and phased-array MRI into noisier data that a corresponding single-coil scanner could have taken. Specifically, we replace the responses from multiple receivers with a linear combination that emulates the response from only a single, aggregate receiver, replete with the low signal-to-noise ratio and phase problems of any single one of the original receivers (combining several receivers is necessary, however, since the original receivers usually have limited spatial sensitivity). This enables experimentation in the simpler context of a si…
Deep learning networks have shown promising results in fast magnetic resonance imaging (MRI) reconstruction. In our work, we develop deep networks to further improve the quantitative and the perceptual quality of reconstruction. To begin with, we propose reconsynergynet (RSN), a network that combines the complementary benefits of independently operating on both the image and the Fourier domain. For a single-coil acquisition, we introduce deep cascade RSN (DC-RSN), a cascade of RSN blocks interleaved with data fidelity (DF) units. Secondly, we improve the structure recovery of DC-RSN for T2 wei…
Cornell University（康奈尔大学）；Weill Medical College of Cornell University（康奈尔大学威尔医学院）
The previously established LOUPE (Learning-based Optimization of the Under-sampling Pattern) framework for optimizing the k-space sampling pattern in MRI was extended in three folds: firstly, fully sampled multi-coil k-space data from the scanner, rather than simulated k-space data from magnitude MR images in LOUPE, was retrospectively under-sampled to optimize the under-sampling pattern of in-vivo k-space data; secondly, binary stochastic k-space sampling, rather than approximate stochastic k-space sampling of LOUPE during training, was applied together with a straight-through (ST) estimator …
University of Minnesota（明尼苏达大学）；University of Florida（佛罗里达大学）；MIT-IBM Watson AI Lab, IBM Research（MIT-IBM沃森人工智能实验室，IBM研究院）
Although deep learning (DL) has received much attention in accelerated MRI, recent studies suggest small perturbations may lead to instabilities in DL-based reconstructions, leading to concern for their clinical application. However, these works focus on single-coil acquisitions, which is not practical. We investigate instabilities caused by small adversarial attacks for multi-coil acquisitions. Our results suggest that, parallel imaging and multi-coil CS exhibit considerable instabilities against small adversarial perturbations.
Facebook AI Research (FAIR)（Facebook人工智能研究院（FAIR））；NYU School of Medicine（纽约大学医学院）
Magnetic Resonance Image (MRI) acquisition is an inherently slow process which has spurred the development of two different acceleration methods: acquiring multiple correlated samples simultaneously (parallel imaging) and acquiring fewer samples than necessary for traditional signal processing methods (compressed sensing). Both methods provide complementary approaches to accelerating the speed of MRI acquisition. In this paper, we present a novel method to integrate traditional parallel imaging methods into deep neural networks that is able to generate high quality reconstructions even for hig…
University of Calgary（卡尔加里大学）；Hotchkiss Brain Institute, University of Calgary（卡尔加里大学霍奇基斯脑研究所）；Foothills Medical Center（山麓医学中心）；Radboud University Medical Center（拉德堡德大学医学中心）；Netherlands Cancer Institute（荷兰癌症研究所）；University of Amsterdam（阿姆斯特丹大学）；Amsterdam UMC（阿姆斯特丹大学医学中心）；University of Campinas（坎皮纳斯大学）
Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-w…
Objective: Concurrent excitation and acquisition in MRI is a method to acquire MRI signal from tissues with very short transverse relaxation time. Since transmit power is many orders of magnitude larger than receive signal, a weak coupling dominates the MR signal during CEA. Thus, appropriate decoupling between transmit and receive coils is required. In this study, two controllable decoupling designs are investigated for achieving isolation between coils. Methods: A modified version of isolation concept used in the full-duplex radios in communication systems is applied to acquire MRI signal us…
University of Oxford（牛津大学）；Siemens Healthineers（西门子医疗）
Magnetic Resonance Imaging (MRI) has excellent soft tissue contrast but is hindered by an inherently slow data acquisition process. Compressed sensing, which reconstructs sparse signals from incoherently sampled data, has been widely applied to accelerate MRI acquisitions. Compressed sensing MRI requires one or more model parameters to be tuned, which is usually done by hand, giving sub-optimal tuning in general. To address this issue, we build on previous work by the authors on the single-coil Variable Density Approximate Message Passing (VDAMP) algorithm, extending the framework to multiple …
Diffusion model is the most advanced method in image generation and has been successfully applied to MRI reconstruction. However, the existing methods do not consider the characteristics of multi-coil acquisition of MRI data. Therefore, we give a new diffusion model, called SPIRiT-Diffusion, based on the SPIRiT iterative reconstruction algorithm. Specifically, SPIRiT-Diffusion characterizes the prior distribution of coil-by-coil images by score matching and characterizes the k-space redundant prior between coils based on self-consistency. With sufficient prior constraint utilized, we achieve s…
Self-supervised training of deep denoisers in multi-coil MRI considering noise correlations
Department of Electrical and Computer Engineering, Seoul National University（电气电子工程系，首尔国立大学）；INMC & IPAI, Seoul National University（INMC与IPAI，首尔国立大学）；Division of Computer Engineering, Hankuk University of Foreign Studies（计算机工程系，韩文大学）；Department of Radiology, Johns Hopkins University School of Medicine（放射科，约翰霍普金斯大学医学院）
Philips Research（飞利浦研究院）；Philips Healthcare（飞利浦医疗）；Leiden University Medical Center（莱顿大学医学中心）
Adaptive intelligence aims at empowering machine learning techniques with the additional use of domain knowledge. In this work, we present the application of adaptive intelligence to accelerate MR acquisition. Starting from undersampled k-space data, an iterative learning-based reconstruction scheme inspired by compressed sensing theory is used to reconstruct the images. We adopt deep neural networks to refine and correct prior reconstruction assumptions given the training data. The network was trained and tested on a knee MRI dataset from the 2019 fastMRI challenge organized by Facebook AI Re…
Microsoft Research（微软研究院）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；University of Minnesota（明尼苏达大学）；Stanford University（斯坦福大学）；Duke University（杜克大学）；New York University（纽约大学）
Improving speed and image quality of Magnetic Resonance Imaging (MRI) via novel reconstruction approaches remains one of the highest impact applications for deep learning in medical imaging. The fastMRI dataset, unique in that it contains large volumes of raw MRI data, has enabled significant advances in accelerating MRI using deep learning-based reconstruction methods. While the impact of the fastMRI dataset on the field of medical imaging is unquestioned, the dataset currently lacks clinical expert pathology annotations, critical to addressing clinically relevant reconstruction frameworks an…
Model-based Dynamic 3D MRI Reconstructions using Neural Fields and Tensor Product Expansions
Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht（MRI治疗与诊断计算成像组，放射治疗系，乌得勒支大学医学中心）
Exploring Siamese Networks in Self-Supervised Fast MRI Reconstruction
Stanford University School of Medicine（斯坦福大学医学院）；Xiamen University（厦门大学）；School of Electronic Science and Engineering, Xiamen University（厦门大学电子科学与工程学院）；School of Informatics, Xiamen University（厦门大学信息学院）；Institute of Artificial Intelligence, Xiamen University（厦门大学人工智能研究院）
University of Florida（佛罗里达大学）；Georgia State University（佐治亚州立大学）
Goal: This work aims at developing a novel calibration-free fast parallel MRI (pMRI) reconstruction method incorporate with discrete-time optimal control framework. The reconstruction model is designed to learn a regularization that combines channels and extracts features by leveraging the information sharing among channels of multi-coil images. We propose to recover both magnitude and phase information by taking advantage of structured convolutional networks in image and Fourier spaces. Methods: We develop a novel variational model with a learnable objective function that integrates an adapti…
University of Birmingham（伯明翰大学）；Imperial College London（帝国理工学院）；MRC London Institute of Medical Sciences（MRC伦敦医学科学研究所）
In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is …
Robust multi-coil MRI reconstruction via self-supervised denoising
Stanford University（斯坦福大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）；Intel Corporation（英特尔公司）；MD Anderson Cancer Center（MD安德森癌症中心）；Dell Medical School Department of Diagnostic Medicine（德克萨斯大学戴维斯医学中心诊断医学系）；Oden Institute for Computational Engineering and Sciences（奥登计算工程与科学研究院）
United Imaging Intelligence（联影智能）；Johns Hopkins University（约翰斯·霍普金斯大学）
Fast and accurate MRI image reconstruction from undersampled data is crucial in clinical practice. Deep learning based reconstruction methods have shown promising advances in recent years. However, recovering fine details from undersampled data is still challenging. In this paper, we introduce a novel deep learning based method, Pyramid Convolutional RNN (PC-RNN), to reconstruct images from multiple scales. Based on the formulation of MRI reconstruction as an inverse problem, we design the PC-RNN model with three convolutional RNN (ConvRNN) modules to iteratively learn the features in multiple…
Cardiovascular MRI (CMR) is a non-invasive imaging modality that provides excellent soft-tissue contrast without the use of ionizing radiation. Physiological motions and limited speed of MRI data acquisition necessitate development of accelerated methods, which typically rely on undersampling. Recovering diagnostic quality CMR images from highly undersampled data has been an active area of research. Recently, several data acquisition and processing methods have been proposed to accelerate CMR. The availability of data to objectively evaluate and compare different reconstruction methods could e…
Friedrich-Alexander University Erlangen-Nuremberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）
In order to ensure trouble-free operation, prediction of hardware failures is essential. This applies especially to medical systems. Our goal is to determine hardware which needs to be exchanged before failing. In this work, we focus on predicting failures of 20-channel Head/Neck coils using image-related measurements. Thus, we aim to solve a classification problem with two classes, normal and broken coil. To solve this problem, we use data of two different levels. One level refers to one-dimensional features per individual coil channel on which we found a fully connected neural network to per…
Netherlands Cancer Institute（荷兰癌症研究所）；qurAI group（qurAI团队）；University of Amsterdam（阿姆斯特丹大学）
Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combi…
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, China（深圳先进技术研究院，中国科学院，中国）；School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, China（生物医学工程学院，深圳大学医学院，深圳大学，中国）；University of Chinese Academy of Sciences, China（中国科学院大学，中国）；Faculty of Computer Science and Artificial Intelligence, Shenzhen University of Advanced Technology, China（计算机科学与人工智能学院，深圳先进技术大学，中国）；State Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, China（生物医学成像科学与系统国家重点实验室，中国科学院，中国）
Purpose: Point-of-care MRI requires operation outside of a faraday shielded room normally used to block image-degrading electromagnetic Interference (EMI). To address this, we introduce the EDITER method, an external sensor based dynamic EMI estimation and removal method to retrospectively remove time-varying external interference sources. Theory and Methods: The method acquires data from multiple EMI detectors (tuned receive coils and electrodes placed on the body) simultaneous with the primary MR coil during image data acquisition. We dynamically calculate impulse response functions that map…
Bangladesh University of Engineering and Technology（孟加拉国工程技术大学）
Parallel imaging accelerates MRI data acquisition by acquiring additional sensitivity information with an array of receiver coils, resulting in fewer phase encoding steps. Because of fewer data requirements than parallel imaging, compressed sensing magnetic resonance imaging (CS-MRI) has gained popularity in the field of medical imaging. Parallel imaging and compressed sensing (CS) both reduce the amount of data captured in the k-space, which speeds up traditional MRI acquisition. As acquisition time is inversely proportional to sample count, forming an image from reduced k-space samples resul…
Friedrich-Alexander University Erlangen-Nuremberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）
Already before systems malfunction one has to know if hardware components will fail in near future in order to counteract in time. Thus, unplanned downtime is ought to be avoided. In medical imaging, maximizing the system's uptime is crucial for patients' health and healthcare provider's daily business. We aim to predict failures of Head/Neck coils used in Magnetic Resonance Imaging (MRI) by training a statistical model on sequential data collected over time. As image features depend on the coil's condition, their deviations from the normal range already hint to future failure. Thus, we used i…
Facebook AI Research (FAIR)（Facebook人工智能研究院（FAIR））；NYU School of Medicine（纽约大学医学院）
The slow acquisition speed of magnetic resonance imaging (MRI) has led to the development of two complementary methods: acquiring multiple views of the anatomy simultaneously (parallel imaging) and acquiring fewer samples than necessary for traditional signal processing methods (compressed sensing). While the combination of these methods has the potential to allow much faster scan times, reconstruction from such undersampled multi-coil data has remained an open problem. In this paper, we present a new approach to this problem that extends previously proposed variational methods by learning ful…
In phase-contrast magnetic resonance imaging (PC-MRI), spin velocity contributes to the phase measured at each voxel. Therefore, estimating velocity from potentially wrapped phase measurements is the task of solving a system of noisy congruence equations. We propose Phase Recovery from Multiple Wrapped Measurements (PRoM) as a fast, approximate maximum likelihood estimator of velocity from multi-coil data with possible amplitude attenuation due to dephasing. The estimator can recover the fullest possible extent of unambiguous velocities, which can greatly exceed twice the highest venc. The est…
The Challenge of Fetal Cardiac MRI Reconstruction Using Deep Learning
King’s College London（伦敦国王学院）；Technical University of Munich（慕尼黑工业大学）；Imperial College London（帝国理工学院）；Guy’s & St. Thomas’ NHS Foundation Trust（盖伊和圣托马斯国民保健服务基金会信托）；Evelina London Children’s Hospital（伊夫琳娜伦敦儿童医院）
Simultaneous multi-slice (SMS) imaging accelerates MRI data acquisition by exciting multiple image slices simultaneously. Overlapping slices are then separated using a mathematical model. Several parameters used in SMS reconstruction impact the quality of final images. Therefore, finding an optimal set of reconstruction parameters is critical to ensure that SMS acceleration does not significantly degrade resulting image quality. Gradient-echo echo planar imaging (EPI) data were acquired with a range of SMS acceleration factors from volunteers. Images were collected using two head coils (a 48-c…
CEA（法国原子能与替代能源委员会）；Inria（法国国家信息与自动化研究所）；AIM（天体物理、物质科学与仪器实验室）；CNRS（法国国家科学研究中心）；Université Paris-Saclay（巴黎萨克雷大学）；Université Paris Diderot（巴黎第七大学）；Sorbonne Paris Cité（巴黎索邦西岱大学）
We present a new neural network, the XPDNet, for MRI reconstruction from periodically under-sampled multi-coil data. We inform the design of this network by taking best practices from MRI reconstruction and computer vision. We show that this network can achieve state-of-the-art reconstruction results, as shown by its ranking of second in the fastMRI 2020 challenge.
Multi-shot echo planar imaging (msEPI) is a promising approach to achieve high in-plane resolution with high sampling efficiency and low T2* blurring. However, due to the geometric distortion, shot-to-shot phase variations and potential subject motion, msEPI continues to be a challenge in MRI. In this work, we introduce acquisition and reconstruction strategies for robust, high-quality msEPI without phase navigators. We propose Blip Up-Down Acquisition (BUDA) using interleaved blip-up and -down phase encoding, and incorporate B0 forward-modeling into Hankel structured low-rank model to enable …
Real-time magnetic resonance imaging (MRI) poses unique challenges related to the speed of data acquisition and to the degree of undersampling necessary to achieve this speed. This Master's thesis introduces and evaluates two pre-processing approaches for these problems: Coil compression to reduce the data volume and a channel selection algorithm to reduce streak artifacts which arise as a consequence of undersampling. Both approaches are tested on real data covering anatomical imaging of the head and of the heart.
Bilkent University（比尔肯特大学）；University of Southern California（南加利福尼亚大学）；Hacettepe University（哈杰泰佩大学）
Learning-based synthetic multi-contrast MRI commonly involves deep models trained using high-quality images of source and target contrasts, regardless of whether source and target domain samples are paired or unpaired. This results in undesirable reliance on fully-sampled acquisitions of all MRI contrasts, which might prove impractical due to limitations on scan costs and time. Here, we propose a novel semi-supervised deep generative model that instead learns to recover high-quality target images directly from accelerated acquisitions of source and target contrasts. To achieve this, the propos…
