Deep learning for accelerated and robust MRI reconstruction.

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction, and focuses on various DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. It explores end-to-end neural networks, pre-trained and generative models, and self-supervised methods, and highlights their contributions to overcoming traditional MRI limitations.

Motion Compensated Unsupervised Deep Learning for 5D MRI.

We propose an unsupervised deep learning algorithm for the motion-compensated reconstruction of 5D cardiac MRI data from 3D radial acquisitions. Ungated free-breathing 5D MRI simplifies the scan planning, improves patient comfort, and offers several clinical benefits over breath-held 2D exams, including isotropic spatial resolution and the ability to reslice the data to arbitrary views. However, the current reconstruction algorithms for 5D MRI take very long computational time, and their outcome is greatly dependent on the uniformity of the binning of the acquired data into different physiological phases.

Prospectively accelerated dynamic speech magnetic resonance imaging at 3 T using a self-navigated spiral-based manifold regularized scheme.

This work develops and evaluates a self-navigated variable density spiral (VDS)-based manifold regularization scheme to prospectively improve dynamic speech magnetic resonance imaging (MRI) at 3 T. Short readout duration spirals (1.3-ms long) were used to minimize sensitivity to off-resonance.

Optimizing Deep Learning for Cardiac MRI Segmentation: The Impact of Automated Slice Range Classification.

Rationale And Objectives: Cardiac magnetic resonance imaging is crucial for diagnosing cardiovascular diseases, but lengthy postprocessing and manual segmentation can lead to observer bias. Deep learning (DL) has been proposed for automated cardiac segmentation; however, its effectiveness is limited by the slice range selection from base to apex.

Materials And Methods: In this study, we integrated an automated slice range classification step to identify basal to apical short-axis slices before DL-based segmentation.

Adapting model-based deep learning to multiple acquisition conditions: Ada-MoDL.

Purpose: The aim of this work is to introduce a single model-based deep network that can provide high-quality reconstructions from undersampled parallel MRI data acquired with multiple sequences, acquisition settings, and field strengths.

Methods: A single unrolled architecture, which offers good reconstructions for multiple acquisition settings, is introduced. The proposed scheme adapts the model to each setting by scaling the convolutional neural network (CNN) features and the regularization parameter with appropriate weights.

Memory-efficient model-based deep learning with convergence and robustness guarantees.

Computational imaging has been revolutionized by compressed sensing algorithms, which offer guaranteed uniqueness, convergence, and stability properties. Model-based deep learning methods that combine imaging physics with learned regularization priors have emerged as more powerful alternatives for image recovery. The main focus of this paper is to introduce a memory efficient model-based algorithm with similar theoretical guarantees as CS methods.

DEEP FACTOR MODEL: A NOVEL APPROACH FOR MOTION COMPENSATED MULTI-DIMENSIONAL MRI.

Recent quantitative parameter mapping methods including MR fingerprinting (MRF) collect a time series of images that capture the evolution of magnetization. The focus of this work is to introduce a novel approach termed as Deep Factor Model(DFM), which offers an efficient representation of the multi-contrast image time series. The higher efficiency of the representation enables the acquisition of the images in a highly undersampled fashion, which translates to reduced scan time in 3D high-resolution multi-contrast applications.

ACCELERATED PARALLEL MRI USING MEMORY EFFICIENT AND ROBUST MONOTONE OPERATOR LEARNING (MOL).

Model-based deep learning methods that combine imaging physics with learned regularization priors have been emerging as powerful tools for parallel MRI acceleration. The main focus of this paper is to determine the utility of the monotone operator learning (MOL) framework in the parallel MRI setting. The MOL algorithm alternates between a gradient descent step using a monotone convolutional neural network (CNN) and a conjugate gradient algorithm to encourage data consistency.

Joint Cardiac Mapping and Cardiac Cine Using Manifold Modeling.

The main focus of this work is to introduce a single free-breathing and ungated imaging protocol to jointly estimate cardiac function and myocardial T1 maps. We reconstruct a time series of images corresponding to k-space data from a free-breathing and ungated inversion recovery gradient echo sequence using a manifold algorithm. We model each image in the time series as a non-linear function of three variables: cardiac and respiratory phases and inversion time.

ENSURE: A General Approach for Unsupervised Training of Deep Image Reconstruction Algorithms.

Image reconstruction using deep learning algorithms offers improved reconstruction quality and lower reconstruction time than classical compressed sensing and model-based algorithms. Unfortunately, clean and fully sampled ground-truth data to train the deep networks is often unavailable in several applications, restricting the applicability of the above methods. We introduce a novel metric termed the ENsemble Stein's Unbiased Risk Estimate (ENSURE) framework, which can be used to train deep image reconstruction algorithms without fully sampled and noise-free images.

Variational Manifold Learning From Incomplete Data: Application to Multislice Dynamic MRI.

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. However, fully sampled data is often unavailable in a variety of problems, including the recovery of dynamic and high-resolution magnetic resonance imaging (MRI). We introduce a novel variational approach to learn a manifold from undersampled data.

Dynamic imaging using motion-compensated smoothness regularization on manifolds (MoCo-SToRM).

. We introduce an unsupervised motion-compensated reconstruction scheme for high-resolution free-breathing pulmonary magnetic resonance imaging..

Dynamic Imaging Using Deep Bi-Linear Unsupervised Representation (DEBLUR).

Bilinear models such as low-rank and dictionary methods, which decompose dynamic data to spatial and temporal factor matrices are powerful and memory-efficient tools for the recovery of dynamic MRI data. Current bilinear methods rely on sparsity and energy compaction priors on the factor matrices to regularize the recovery. Motivated by deep image prior, we introduce a novel bilinear model, whose factor matrices are generated using convolutional neural networks (CNNs).

Multi-band- and in-plane-accelerated diffusion MRI enabled by model-based deep learning in q-space and its extension to learning in the spherical harmonic domain.

Purpose: To propose a new method for the recovery of combined in-plane- and multi-band (MB)-accelerated diffusion MRI data.

Methods: Combining MB acceleration with in-plane acceleration is crucial to improve the time efficiency of high (angular and spatial) resolution diffusion scans. However, as the MB factor and in-plane acceleration increase, the reconstruction becomes challenging due to the heavy aliasing.

DYNAMIC IMAGING USING DEEP BILINEAR UNSUPERVISED LEARNING (DEBLUR).

Bilinear models such as low-rank and compressed sensing, which decompose the dynamic data to spatial and temporal factors, are powerful and memory efficient tools for the recovery of dynamic MRI data. These methods rely on sparsity and energy compaction priors on the factors to regularize the recovery. Motivated by deep image prior, we introduce a novel bilinear model, whose factors are regularized using convolutional neural networks.

RECONSTRUCTION AND SEGMENTATION OF PARALLEL MR DATA USING IMAGE DOMAIN DEEP-SLR.

The main focus of this work is a novel framework for the joint reconstruction and segmentation of parallel MRI (PMRI) brain data. We introduce an image domain deep network for calibrationless recovery of undersampled PMRI data. The proposed approach is the deep-learning (DL) based generalization of local low-rank based approaches for uncalibrated PMRI recovery including CLEAR [6].

DEEP GENERATIVE STORM MODEL FOR DYNAMIC IMAGING.

We introduce a novel generative smoothness regularization on manifolds (SToRM) model for the recovery of dynamic image data from highly undersampled measurements. The proposed generative framework represents the image time series as a smooth non-linear function of low-dimensional latent vectors that capture the cardiac and respiratory phases. The non-linear function is represented using a deep convolutional neural network (CNN).

Recovery of surfaces and functions in high dimensions: sampling theory and links to neural networks.

Several imaging algorithms including patch-based image denoising, image time series recovery, and convolutional neural networks can be thought of as methods that exploit the manifold structure of signals. While the empirical performance of these algorithms is impressive, the understanding of recovery of the signals and functions that live on manifold is less understood. In this paper, we focus on the recovery of signals that live on a union of surfaces.

ENSURE: ENSEMBLE STEIN'S UNBIASED RISK ESTIMATOR FOR UNSUPERVISED LEARNING.

Deep learning algorithms are emerging as powerful alternatives to compressed sensing methods, offering improved image quality and computational efficiency. Unfortunately, fully sampled training images may not be available or are difficult to acquire in several applications, including high-resolution and dynamic imaging. Previous studies in image reconstruction have utilized Stein's Unbiased Risk Estimator (SURE) as a mean square error (MSE) estimate for the image denoising step in an unrolled network.

Radiomics side experiments and DAFIT approach in identifying pulmonary hypertension using Cardiac MRI derived radiomics based machine learning models.

Side experiments are performed on radiomics models to improve their reproducibility. We measure the impact of myocardial masks, radiomic side experiments and data augmentation for information transfer (DAFIT) approach to differentiate patients with and without pulmonary hypertension (PH) using cardiac MRI (CMRI) derived radiomics. Feature extraction was performed from the left ventricle (LV) and right ventricle (RV) myocardial masks using CMRI in 82 patients (42 PH and 40 controls).

Radiomics Detection of Pulmonary Hypertension via Texture-Based Assessments of Cardiac MRI: A Machine-Learning Model Comparison-Cardiac MRI Radiomics in Pulmonary Hypertension.

The role of reliable, non-invasive imaging-based recognition of pulmonary hypertension (PH) remains a diagnostic challenge. The aim of the current pilot radiomics study was to assess the diagnostic performance of cardiac MRI (cMRI)-based texture features to accurately predict PH. The study involved IRB-approved retrospective analysis of cMRIs from 72 patients (42 PH and 30 healthy controls) for the primary analysis.

qModeL: A plug-and-play model-based reconstruction for highly accelerated multi-shot diffusion MRI using learned priors.

Purpose: To introduce a joint reconstruction method for highly undersampled multi-shot diffusion weighted (msDW) scans.

Methods: Multi-shot EPI methods enable higher spatial resolution for diffusion MRI, but at the expense of long scan-time. Highly accelerated msDW scans are needed to enable their utilization in advanced microstructure studies, which require high q-space coverage.

Dynamic Imaging Using a Deep Generative SToRM (Gen-SToRM) Model.

We introduce a generative smoothness regularization on manifolds (SToRM) model for the recovery of dynamic image data from highly undersampled measurements. The model assumes that the images in the dataset are non-linear mappings of low-dimensional latent vectors. We use the deep convolutional neural network (CNN) to represent the non-linear transformation.