We propose a deep self-learning algorithm to learn the manifold structure of free-breathing and ungated cardiac data and to recover the cardiac CINE MRI from highly undersampled measurements. Our method learns the manifold structure in the dynamic data from navigators using autoencoder network. The trained autoencoder is then used as a prior in the image reconstruction framework. We have tested the proposed method on free-breathing and ungated cardiac CINE data, which is acquired using a navigated golden-angle gradient-echo radial sequence. Results show the ability of our method to better capture the manifold structure, thus providing us reduced spatial and temporal blurring as compared to the SToRM reconstruction.
Current deep learning-based manifold learning algorithms such as the variational autoencoder (VAE) require fully sampled data to learn the probability density of real-world datasets. Once learned, the density can be used for a variety of tasks, including data imputation. However, fully sampled data is often unavailable in a variety of problems, including the recovery of dynamic and high-resolution MRI data considered in this work. To overcome this problem, we introduce a novel variational approach to learn a manifold from undersampled data. The VAE uses a decoder fed by latent vectors, drawn f…
Plug-and-play (PnP) methods that employ application-specific denoisers have been proposed to solve inverse problems, including MRI reconstruction. However, training application-specific denoisers is not feasible for many applications due to the lack of training data. In this work, we propose a PnP-inspired recovery method that does not require data beyond the single, incomplete set of measurements. The proposed method, called recovery with a self-calibrated denoiser (ReSiDe), trains the denoiser from the patches of the image being recovered. The denoiser training and a call to the denoising su…
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…
University at Buffalo（布法罗大学）；INRIA（法国国家信息与自动化研究所）；Université Côte d’ Azur（蔚蓝海岸大学）；Stanford University（斯坦福大学）；Purdue University（普渡大学）
This paper puts forth a novel bi-linear modeling framework for data recovery via manifold-learning and sparse-approximation arguments and considers its application to dynamic magnetic-resonance imaging (dMRI). Each temporal-domain MR image is viewed as a point that lies onto or close to a smooth manifold, and landmark points are identified to describe the point cloud concisely. To facilitate computations, a dimensionality reduction module generates low-dimensional/compressed renditions of the landmark points. Recovery of the high-fidelity MRI data is realized by solving a non-convex minimizati…
University at Buffalo（布法罗大学）；Stanford University（斯坦福大学）；Purdue University（普渡大学）
This paper establishes a kernel-based framework for reconstructing data on manifolds, tailored to fit the dynamic-(d)MRI-data recovery problem. The proposed methodology exploits simple tangent-space geometries of manifolds in reproducing kernel Hilbert spaces and follows classical kernel-approximation arguments to form the data-recovery task as a bi-linear inverse problem. Departing from mainstream approaches, the proposed methodology uses no training data, employs no graph Laplacian matrix to penalize the optimization task, uses no costly (kernel) pre-imaging step to map feature points back t…
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；Inner Mongolia University（内蒙古大学）
Recently, score-based diffusion models have shown satisfactory performance in MRI reconstruction. Most of these methods require a large amount of fully sampled MRI data as a training set, which, sometimes, is difficult to acquire in practice. This paper proposes a fully-sampled-data-free score-based diffusion model for MRI reconstruction, which learns the fully sampled MR image prior in a self-supervised manner on undersampled data. Specifically, we first infer the fully sampled MR image distribution from the undersampled data by Bayesian deep learning, then perturb the data distribution and a…
Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising…
This study aims to accelerate coronary MRI using a novel reconstruction algorithm, called self-consistent robust artificial-neural-networks for k-space interpolation (sRAKI). sRAKI performs iterative parallel imaging reconstruction by enforcing coil self-consistency using subject-specific neural networks. This approach extends the linear convolutions in SPIRiT to nonlinear interpolation using convolutional neural networks (CNNs). These CNNs are trained individually for each scan using the scan-specific autocalibrating signal (ACS) data. Reconstruction is performed by imposing the learned self-…
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）
The University of Iowa（爱荷华大学）；University of Wisconsin at Madison（威斯康星大学麦迪逊分校）
We introduce an unsupervised deep manifold learning algorithm for motion-compensated dynamic MRI. We assume that the motion fields in a free-breathing lung MRI dataset live on a manifold. The motion field at each time instant is modeled as the output of a deep generative model, driven by low-dimensional time-varying latent vectors that capture the temporal variability. The images at each time instant are modeled as the deformed version of an image template using the above motion fields. The template, the parameters of the deep generator, and the latent vectors are learned from the k-t space da…
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）
Self-supervised models allow (pre-)training on unlabeled data and therefore have the potential to overcome the need for large annotated cohorts. One leading self-supervised model is the masked autoencoder (MAE) which was developed on natural imaging data. The MAE is masking out a high fraction of visual transformer (ViT) input patches, to then recover the uncorrupted images as a pretraining task. In this work, we extend MAE to perform anomaly detection on breast magnetic resonance imaging (MRI). This new model, coined masked autoencoder for medical imaging (MAEMI) is trained on two non-contras…
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…
Yonsei University（延世大学）；GE Healthcare（通用电气医疗）；Seoul National University Hospital（首尔大学医院）
In this paper, we develop an efficient retrospective deep learning method called stacked U-Nets with self-assisted priors to address the problem of rigid motion artifacts in MRI. The proposed work exploits the usage of additional knowledge priors from the corrupted images themselves without the need for additional contrast data. The proposed network learns missed structural details through sharing auxiliary information from the contiguous slices of the same distorted subject. We further design a refinement stacked U-Nets that facilitates preserving of the image spatial details and hence improv…
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 …
MIT（麻省理工学院）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）
Fetal motion is unpredictable and rapid on the scale of conventional MR scan times. Therefore, dynamic fetal MRI, which aims at capturing fetal motion and dynamics of fetal function, is limited to fast imaging techniques with compromises in image quality and resolution. Super-resolution for dynamic fetal MRI is still a challenge, especially when multi-oriented stacks of image slices for oversampling are not available and high temporal resolution for recording the dynamics of the fetus or placenta is desired. Further, fetal motion makes it difficult to acquire high-resolution images for supervi…
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…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Automated segmentation of multiple sclerosis (MS) lesions from MRI scans is important to quantify disease progression. In recent years, convolutional neural networks (CNNs) have shown top performance for this task when a large amount of labeled data is available. However, the accuracy of CNNs suffers when dealing with few and/or sparsely labeled datasets. A potential solution is to leverage the information available in large public datasets in conjunction with a target dataset which only has limited labeled data. In this paper, we propose a training framework, SSL2 (self-supervised-semi-superv…
Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled traini…
Self-supervised learning has shown great promise due to its capability to train deep learning MRI reconstruction methods without fully-sampled data. Current self-supervised learning methods for physics-guided reconstruction networks split acquired undersampled data into two disjoint sets, where one is used for data consistency (DC) in the unrolled network and the other to define the training loss. In this study, we propose an improved self-supervised learning strategy that more efficiently uses the acquired data to train a physics-guided reconstruction network without a database of fully-sampl…
Compressed sensing has reinvigorated the field of non-Cartesian sampling in magnetic resonance imaging (MRI). Until now there has been no 3D radial view-order which meets all the desired characteristics for simultaneous dynamic/high-resolution imaging, such as for self-navigated motion-corrected high resolution neuroimaging. In this work, we examine the use of Hierarchical Equal Area iso-Latitude Pixelization (HEALPix) for generation of three-dimensional (3D) radial view-orders for MRI, and compare to a selection of commonly used 3D view-orders. The resulting trajectories were evaluated throug…
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）；University of Chinese Academy of Sciences（中国科学院大学）；Peng Cheng Laboratory（鹏城实验室）
Magnetic Resonance Imaging (MRI) has become an important technique in the clinic for the visualization, detection, and diagnosis of various diseases. However, one bottleneck limitation of MRI is the relatively slow data acquisition process. Fast MRI based on k-space undersampling and high-quality image reconstruction has been widely utilized, and many deep learning-based methods have been developed in recent years. Although promising results have been achieved, most existing methods require fully-sampled reference data for training the deep learning models. Unfortunately, fully-sampled MRI dat…
Swiss Federal Institute of Technology (ETH) Zürich（苏黎世联邦理工学院）；Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins School of Medicine（约翰斯·霍普金斯大学医学院）；University of Maryland School of Medicine（马里兰大学医学院）
The thalamus is a subcortical gray matter structure that plays a key role in relaying sensory and motor signals within the brain. Its nuclei can atrophy or otherwise be affected by neurological disease and injuries including mild traumatic brain injury. Segmenting both the thalamus and its nuclei is challenging because of the relatively low contrast within and around the thalamus in conventional magnetic resonance (MR) images. This paper explores imaging features to determine key tissue signatures that naturally cluster, from which we can parcellate thalamic nuclei. Tissue contrasts include T1…
Self-Supervised Joint Reconstruction and Denoising of T2-Weighted PROPELLER MRI of the Lungs at 0.55T
New York University Grossman School of Medicine（纽约大学格罗斯曼医学院）；New York University Tandon School of Engineering（纽约大学坦登工程学院）；Indiana University School of Medicine（印第安纳大学医学院）
Improved Multi-Shot Diffusion-Weighted MRI with Zero-Shot Self-Supervised Learning Reconstruction
Athinoula A. Martinos Center for Biomedical Imaging（阿瑟诺拉·A·马蒂诺斯生物医学成像中心）；Harvard Medical School（哈佛医学院）；University of São Paulo（圣保罗大学）；Technische Universität München（慕尼黑工业大学）；Harvard-MIT Health Sciences and Technology（哈佛-麻省理工健康科学与技术部）
We present a method for estimating intravoxel parameters from a DW-MRI based on deep learning techniques. We show that neural networks (DNNs) have the potential to extract information from diffusion-weighted signals to reconstruct cerebral tracts. We present two DNN models: one that estimates the axonal structure in the form of a voxel and the other to calculate the structure of the central voxel using the voxel neighborhood. Our methods are based on a proposed parameter representation suitable for the problem. Since it is practically impossible to have real tagged data for any acquisition pro…
Dual-domain Multi-path Self-supervised Diffusion Model for Accelerated MRI Reconstruction
Department of Radiology, Northwestern University（放射科，西北大学）；Department of Biomedical Engineering, Huazhong University of Science and Technology（生物医学工程系，华中科技大学）
Image Quality Assessment (IQA) is of great value in the workflow of Magnetic Resonance Imaging (MRI)-based analysis. Blind IQA (BIQA) methods are especially required since high-quality reference MRI images are usually not available. Recently, many efforts have been devoted to developing deep learning-based BIQA approaches. However, the performance of these methods is limited due to the utilization of simple content-non-adaptive network parameters and the waste of the important 3D spatial information of the medical images. To address these issues, we design a 3D content-adaptive hyper-network f…
Self-Supervised Diffusion MRI Denoising via Iterative and Stable Refinement
School of Biomedical Engineering, Division of Life Sciences and Medicine, USTC（中国科学技术大学生命科学与医学部生物医学工程学院）；MIRACLE Center, Suzhou Institute for Advance Research, USTC（中国科学技术大学苏州研究院MIRACLE中心）；State Key Laboratory of Precision and Intelligent Chemistry, USTC（中国科学技术大学精准与智能化学国家重点实验室）；Key Laboratory of Intelligent Information Processing of CAS, Institute of Computing Technology, CAS（中国科学院计算技术研究所中国科学院智能信息处理重点实验室）
Fetal brain magnetic resonance imaging (MRI) offers exquisite images of the developing brain but is not suitable for anomaly screening. For this ultrasound (US) is employed. While expert sonographers are adept at reading US images, MR images are much easier for non-experts to interpret. Hence in this paper we seek to produce images with MRI-like appearance directly from clinical US images. Our own clinical motivation is to seek a way to communicate US findings to patients or clinical professionals unfamiliar with US, but in medical image analysis such a capability is potentially useful, for in…
