Deep learning (DL) based unrolled reconstructions have shown state-of-the-art performance for under-sampled magnetic resonance imaging (MRI). Similar to compressed sensing, DL can leverage high-dimensional data (e.g. 3D, 2D+time, 3D+time) to further improve performance. However, network size and depth are currently limited by the GPU memory required for backpropagation. Here we use a memory-efficient learning (MEL) framework which favorably trades off storage with a manageable increase in computation during training. Using MEL with multi-dimensional data, we demonstrate improved image reconstruction performance for in-vivo 3D MRI and 2D+time cardiac cine MRI. MEL uses far less GPU memory while marginally increasing the training time, which enables new applications of DL to high-dimensional MRI.
Harvard Medical School(哈佛医学院);Boston Children’s Hospital(波士顿儿童医院)
Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. Conventional MRI reconstruction methods for fast MRI acquisition mostly relied on different regularizers which represent analytical models of sparsity. However, recent data-driven methods based on deep learning has resulted in promising improvements in image reconstruction algorithms. In this paper, we propose a deep plug-and-play prior framework for parallel MRI reconstruction problems which utilize a deep neural network (DNN) as an advanced d…
Pseudo-MRI-Guided PET Image Reconstruction Method Based on a Diffusion Probabilistic Model
Washington University in St. Louis(圣路易斯华盛顿大学);Yale University(耶鲁大学);Western University(西安大略大学);Lawson Health Research Institute(劳森健康研究所);McGill University(麦吉尔大学);Siemens Healthineers AG(西门子医疗保健公司);Mallinckrodt Institute of Radiology(马林克罗特放射学研究所)
Deep learning based on unrolled algorithm has served as an effective method for accelerated magnetic resonance imaging (MRI). However, many methods ignore the direct use of edge information to assist MRI reconstruction. In this work, we present the edge-weighted pFISTA-Net that directly applies the detected edge map to the soft-thresholding part of pFISTA-Net. The soft-thresholding value of different regions will be adjusted according to the edge map. Experimental results of a public brain dataset show that the proposed yields reconstructions with lower error and better artifact suppression co…
Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. The data-driven methods based on deep neural networks have resulted in promising improvements, compared to the conventional methods, in image reconstruction algorithms. The connection between deep neural network and Ordinary Differential Equation (ODE) has been observed and studied recently. The studies show that different residual networks can be interpreted as Euler discretization of an ODE. In this paper, we propose an ODE-based deep network…
Cornell University(康奈尔大学);Massachusetts Institute of Technology(麻省理工学院);Massachusetts General Hospital(麻省总医院);Harvard Medical School(哈佛医学院)
Reconstructing under-sampled k-space measurements in Compressed Sensing MRI (CS-MRI) is classically solved with regularized least-squares. Recently, deep learning has been used to amortize this optimization by training reconstruction networks on a dataset of under-sampled measurements. Here, a crucial design choice is the regularization function(s) and corresponding weight(s). In this paper, we explore a novel strategy of using a hypernetwork to generate the parameters of a separate reconstruction network as a function of the regularization weight(s), resulting in a regularization-agnostic rec…
Hybrid Learning: A Novel Combination of Self-Supervised and Supervised Learning for Joint MRI Reconstruction and Denoising in Low-Field MRI
New York University Grossman School of Medicine(纽约大学格罗斯曼医学院);NYU Tandon School of Engineering(纽约大学坦登工程学院);Icahn School of Medicine at Mount Sinai(西奈山伊坎医学院)
Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clini…
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…
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)
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…
This paper considers the problem of undersampled MRI reconstruction. We propose a novel Transformer-based framework for directly processing signal in k-space, going beyond the limitation of regular grids as ConvNets do. We adopt an implicit representation of k-space spectrogram, treating spatial coordinates as inputs, and dynamically query the sparsely sampled points to reconstruct the spectrogram, i.e. learning the inductive bias in k-space. To strike a balance between computational cost and reconstruction quality, we build the decoder with hierarchical structure to generate low-resolution an…
Peking University Shenzhen Graduate School(北京大学深圳研究生院);Peng Cheng Laboratory(鹏城实验室);Harbin Institute of Technology (Shenzhen)(哈尔滨工业大学(深圳));Tsinghua University(清华大学)
Compressed Sensing MRI (CS-MRI) aims at reconstructing de-aliased images from sub-Nyquist sampling k-space data to accelerate MR Imaging, thus presenting two basic issues, i.e., where to sample and how to reconstruct. To deal with both problems simultaneously, we propose a novel end-to-end Probabilistic Under-sampling and Explicable Reconstruction neTwork, dubbed PUERT, to jointly optimize the sampling pattern and the reconstruction network. Instead of learning a deterministic mask, the proposed sampling subnet explores an optimal probabilistic sub-sampling pattern, which describes independent…
Accelerating magnetic resonance image (MRI) reconstruction process is a challenging ill-posed inverse problem due to the excessive under-sampling operation in k-space. In this paper, we propose a recurrent transformer model, namely ReconFormer, for MRI reconstruction which can iteratively reconstruct high fertility magnetic resonance images from highly under-sampled k-space data. In particular, the proposed architecture is built upon Recurrent Pyramid Transformer Layers (RPTL), which jointly exploits intrinsic multi-scale information at every architecture unit as well as the dependencies of th…
United Imaging Intelligence(联影智能);UIH America, Inc.(联影美国公司);United Imaging Healthcare(联影医疗)
Retrospectively gated cine (retro-cine) MRI is the clinical standard for cardiac functional analysis. Deep learning (DL) based methods have been proposed for the reconstruction of highly undersampled MRI data and show superior image quality and magnitude faster reconstruction time than CS-based methods. Nevertheless, it remains unclear whether DL reconstruction is suitable for cardiac function analysis. To address this question, in this study we evaluate and compare the cardiac functional values (EDV, ESV and EF for LV and RV, respectively) obtained from highly accelerated MRI acquisition usin…
Shanghai Jiao Tong University(上海交通大学);Shanghai United Imaging Intelligence Co., Ltd.(上海联影智能科技有限公司);ShanghaiTech University(上海科技大学)
In clinical practice, multi-modal magnetic resonance imaging (MRI) with different contrasts is usually acquired in a single study to assess different properties of the same region of interest in the human body. The whole acquisition process can be accelerated by having one or more modalities under-sampled in the $k$-space. Recent research has shown that, considering the redundancy between different modalities, a target MRI modality under-sampled in the $k$-space can be more efficiently reconstructed with a fully-sampled reference MRI modality. However, we find that the performance of the afore…
University of Chinese Academy of Sciences(中国科学院大学);Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences(中国科学院深圳先进技术研究院);Pengcheng Laboratory(鹏城实验室);Shenzhen University(深圳大学);Nanchang University(南昌大学)
Recovering high-quality images from undersampled measurements is critical for accelerated MRI reconstruction. Recently, various supervised deep learning-based MRI reconstruction methods have been developed. Despite the achieved promising performances, these methods require fully sampled reference data, the acquisition of which is resource-intensive and time-consuming. Self-supervised learning has emerged as a promising solution to alleviate the reliance on fully sampled datasets. However, existing self-supervised methods suffer from reconstruction errors due to the insufficient constraint enfo…
The University of Queensland(昆士兰大学);The Commonwealth Scientific and Industrial Research Organisation(联邦科学与工业研究组织);Johns Hopkins University(约翰斯·霍普金斯大学);University of Science and Technology of China(中国科学技术大学)
Magnetic resonance (MR) images exhibit various contrasts and appearances based on factors such as different acquisition protocols, views, manufacturers, scanning parameters, etc. This generally accessible appearance-related side information affects deep learning-based undersampled magnetic resonance imaging (MRI) reconstruction frameworks, but has been overlooked in the majority of current works. In this paper, we investigate the use of such side information as normalisation parameters in a convolutional neural network (CNN) to improve undersampled MRI reconstruction. Specifically, a Side Info…
University of Iowa(爱荷华大学);Philips HealthCare(飞利浦医疗);University of Wisconsin(威斯康星大学);GE HealthCare(通用电气医疗)
Free-breathing cardiac MRI schemes are emerging as competitive alternatives to breath-held cine MRI protocols, enabling applicability to pediatric and other population groups that cannot hold their breath. Because the data from the slices are acquired sequentially, the cardiac/respiratory motion patterns may be different for each slice; current free-breathing approaches perform independent recovery of each slice. In addition to not being able to exploit the inter-slice redundancies, manual intervention or sophisticated post-processing methods are needed to align the images post-recovery for qu…
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…
Purpose: To develop a synergistic image reconstruction framework that exploits multicontrast (MC), multicoil, and compressed sensing (CS) redundancies in magnetic resonance imaging (MRI). Approach: CS, MC acquisition, and parallel imaging (PI) have been individually well developed, but the combination of the three has not been equally well studied, much less the potential benefits of isotropy within such a setting. Inspired by total variation theory, we introduce an isotropic MC image regularizer and attain its full potential by integrating it into compressed MC multicoil MRI. A convex optimiz…
Tsinghua Shenzhen International Graduate School, Tsinghua University(清华大学深圳国际研究生院);Tencent AI Lab(腾讯人工智能实验室);The Chinese University of Hong Kong(香港中文大学);University of Texas at Arlington(德克萨斯大学阿灵顿分校)
Recently, deep neural networks have greatly advanced undersampled Magnetic Resonance Image (MRI) reconstruction, wherein most studies follow the one-anatomy-one-network fashion, i.e., each expert network is trained and evaluated for a specific anatomy. Apart from inefficiency in training multiple independent models, such convention ignores the shared de-aliasing knowledge across various anatomies which can benefit each other. To explore the shared knowledge, one naive way is to combine all the data from various anatomies to train an all-round network. Unfortunately, despite the existence of th…
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 …
The University of Queensland(昆士兰大学);Griffith University(格里菲斯大学)
MRI images of the same subject in different contrasts contain shared information, such as the anatomical structure. Utilizing the redundant information amongst the contrasts to sub-sample and faithfully reconstruct multi-contrast images could greatly accelerate the imaging speed, improve image quality and shorten scanning protocols. We propose an algorithm that generates the optimised sampling pattern and reconstruction scheme of one contrast (e.g. T2-weighted image) when images with different contrast (e.g. T1-weighted image) have been acquired. The proposed algorithm achieves increased PSNR …
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)
Technion – Israel Institute of Technology(以色列理工学院)
Uncertainty quantification in deep-learning (DL) based image reconstruction models is critical for reliable clinical decision making based on the reconstructed images. We introduce "NPB-REC", a non-parametric fully Bayesian framework for uncertainty assessment in MRI reconstruction from undersampled "k-space" data. We use Stochastic gradient Langevin dynamics (SGLD) during the training phase to characterize the posterior distribution of the network weights. We demonstrated the added-value of our approach on the multi-coil brain MRI dataset, from the fastmri challenge, in comparison to the base…
Lightweight Hypercomplex MRI Reconstruction: A Generalized Kronecker-Parameterized Approach
Bioengineering Department(生物工程系);Imperial-X, Imperial College London(帝国理工学院Imperial-X);Imperial College London(帝国理工学院);National Heart and Lung Institute, Imperial College London(国家心脏和肺 institute, 帝国理工学院);Cardiovascular Research Centre, Royal Brompton Hospital(心血管研究中心, 罗伊·布罗姆普顿医院);School of Biomedical Engineering and Imaging Sciences, King’s College London(生物医学工程与成像科学学院, 伦敦国王学院)
The need for fast acquisition and automatic analysis of MRI data is growing in the age of big data. Although compressed sensing magnetic resonance imaging (CS-MRI) has been studied to accelerate MRI by reducing k-space measurements, in current CS-MRI techniques MRI applications such as segmentation are overlooked when doing image reconstruction. In this paper, we test the utility of CS-MRI methods in automatic segmentation models and propose a unified deep neural network architecture called SegNetMRI which we apply to the combined CS-MRI reconstruction and segmentation problem. SegNetMRI is bu…
Facebook AI Research(Facebook人工智能研究);fastMRI team(fastMRI团队)
Deep learning approaches to accelerated MRI take a matrix of sampled Fourier-space lines as input and produce a spatial image as output. In this work we show that by careful choice of the offset used in the sampling procedure, the symmetries in k-space can be better exploited, producing higher quality reconstructions than given by standard equally-spaced samples or randomized samples motivated by compressed sensing.
Yale University(耶鲁大学);New York University(纽约大学);Hyperfine Research(Hyperfine研究公司)
Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptima…
Faculty of Computer Science, Otto-von-Guericke University Magdeburg(马格德堡奥托·冯·格里克大学计算机科学学院);Clinic for Radiology and Nuclear Medicine, University Hospital Magdeburg(马格德堡大学医院放射与核医学诊所)
Purpose: We aim to develop a robust 4D MRI method for large FOVs enabling the extraction of irregular respiratory motion that is readily usable with all MRI machines and thus applicable to support a wide range of interventional settings. Method: We propose a 4D MRI reconstruction method to capture an arbitrary number of breathing states. It uses template updates in navigator slices and search regions for fast and robust vessel cross-section tracking. It captures FOVs of 255 mm x 320 mm x 228 mm at a spatial resolution of 1.82 mm x 1.82 mm x 4mm and temporal resolution of 200ms. A total of 37 4…
The volume estimation of brain regions from MRI data is a key problem in many clinical applications, where the acquisition of data at high spatial resolution is desirable. While parallel MRI and constrained image reconstruction algorithms can accelerate the scans, image reconstruction artifacts are inevitable, especially at high acceleration factors. We introduce a novel image domain deep-learning framework for calibrationless parallel MRI reconstruction, coupled with a segmentation network to improve image quality and to reduce the vulnerability of current segmentation algorithms to image art…
University of Florida(佛罗里达大学);Facebook AI Research(脸书人工智能研究院);NYU School of Medicine(纽约大学医学院)
The goal of MRI reconstruction is to restore a high fidelity image from partially observed measurements. This partial view naturally induces reconstruction uncertainty that can only be reduced by acquiring additional measurements. In this paper, we present a novel method for MRI reconstruction that, at inference time, dynamically selects the measurements to take and iteratively refines the prediction in order to best reduce the reconstruction error and, thus, its uncertainty. We validate our method on a large scale knee MRI dataset, as well as on ImageNet. Results show that (1) our system succ…
Hyperfine Research(Hyperfine研究院);Yale University(耶鲁大学);New York University(纽约大学)
While enabling accelerated acquisition and improved reconstruction accuracy, current deep MRI reconstruction networks are typically supervised, require fully sampled data, and are limited to Cartesian sampling patterns. These factors limit their practical adoption as fully-sampled MRI is prohibitively time-consuming to acquire clinically. Further, non-Cartesian sampling patterns are particularly desirable as they are more amenable to acceleration and show improved motion robustness. To this end, we present a fully self-supervised approach for accelerated non-Cartesian MRI reconstruction which …
Bilkent University(比尔肯特大学);National Magnetic Resonance Research Center, Bilkent University(比尔肯特大学国家磁共振研究中心)
Supervised reconstruction models are characteristically trained on matched pairs of undersampled and fully-sampled data to capture an MRI prior, along with supervision regarding the imaging operator to enforce data consistency. To reduce supervision requirements, the recent deep image prior framework instead conjoins untrained MRI priors with the imaging operator during inference. Yet, canonical convolutional architectures are suboptimal in capturing long-range relationships, and priors based on randomly initialized networks may yield suboptimal performance. To address these limitations, here …
Although deep learning (DL) has gained much popularity for accelerated magnetic resonance imaging (MRI), recent studies have shown that DL-based MRI reconstruction models could be oversensitive to tiny input perturbations (that are called 'adversarial perturbations'), which cause unstable, low-quality reconstructed images. This raises the question of how to design robust DL methods for MRI reconstruction. To address this problem, we propose a novel image reconstruction framework, termed SMOOTHED UNROLLING (SMUG), which advances a deep unrolling-based MRI reconstruction model using a randomized…
Yale University(耶鲁大学);United Imaging Intelligence(联影智能);University of Georgia(佐治亚大学)
High-quality MRI reconstruction plays a critical role in clinical applications. Deep learning-based methods have achieved promising results on MRI reconstruction. However, most state-of-the-art methods were designed to optimize the evaluation metrics commonly used for natural images, such as PSNR and SSIM, whereas the visual quality is not primarily pursued. Compared to the fully-sampled images, the reconstructed images are often blurry, where high-frequency features might not be sharp enough for confident clinical diagnosis. To this end, we propose an invertible sharpening network (InvSharpNe…
Parallel imaging is a widely-used technique to accelerate magnetic resonance imaging (MRI). However, current methods still perform poorly in reconstructing artifact-free MRI images from highly undersampled k-space data. Recently, implicit neural representation (INR) has emerged as a new deep learning paradigm for learning the internal continuity of an object. In this study, we adopted INR to parallel MRI reconstruction. The MRI image was modeled as a continuous function of spatial coordinates. This function was parameterized by a neural network and learned directly from the measured k-space it…
Bilkent University(比尔肯特大学);University of Southern California(南加州大学)
Multi-institutional efforts can facilitate training of deep MRI reconstruction models, albeit privacy risks arise during cross-site sharing of imaging data. Federated learning (FL) has recently been introduced to address privacy concerns by enabling distributed training without transfer of imaging data. Existing FL methods for MRI reconstruction employ conditional models to map from undersampled to fully-sampled acquisitions via explicit knowledge of the imaging operator. Since conditional models generalize poorly across different acceleration rates or sampling densities, imaging operators mus…
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.
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)
Deep learning techniques have emerged as a promising approach to highly accelerated MRI. However, recent reconstruction challenges have shown several drawbacks in current deep learning approaches, including the loss of fine image details even using models that perform well in terms of global quality metrics. In this study, we propose an end-to-end deep learning framework for image reconstruction and pathology detection, which enables a clinically aware evaluation of deep learning reconstruction quality. The solution is demonstrated for a use case in detecting meniscal tears on knee MRI studies…
Indraprastha Institute of Information Technology(英迪拉·普拉斯特哈信息技术研究所)
In this work we address the problem of real-time dynamic MRI reconstruction. There are a handful of studies on this topic; these techniques are either based on compressed sensing or employ Kalman Filtering. These techniques cannot achieve the reconstruction speed necessary for real-time reconstruction. In this work, we propose a new approach to MRI reconstruction. We learn a non-linear mapping from the unstructured aliased images to the corresponding clean images using a stacked denoising autoencoder (SDAE). The training for SDAE is slow, but the reconstruction is very fast - only requiring a …
Phase-contrast magnetic resonance imaging (MRI) provides time-resolved quantification of blood flow dynamics that can aid clinical diagnosis. Long in vivo scan times due to repeated three-dimensional (3D) volume sampling over cardiac phases and breathing cycles necessitate accelerated imaging techniques that leverage data correlations. Standard compressed sensing reconstruction methods require tuning of hyperparameters and are computationally expensive, which diminishes the potential reduction of examination times. We propose an efficient model-based deep neural reconstruction network and eval…
DUN-SRE: Deep Unrolling Network with Spatiotemporal Rotation Equivariance for Dynamic MRI Reconstruction
University of Nottingham Ningbo China(诺丁汉大学宁波校区);Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences(深圳先进技术研究院);School of Mathematics and Statistics, Xi’an Jiaotong University(西安交通大学数学与统计学院)
Computational Radiology Laboratory, Boston Children’s Hospital(波士顿儿童医院计算放射实验室);Harvard Medical School(哈佛医学院)
Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. Recently, the deep learning-based MRI reconstruction techniques were suggested to accelerate MR image acquisition. The most common issues in any deep learning-based MRI reconstruction approaches are generalizability and transferability. For different MRI scanner configurations using these approaches, the network must be trained from scratch every time with new training dataset, acquired under new configurations, to be able to provide good recon…