On the Foundation Model for Cardiac MRI Reconstruction

In recent years, machine learning (ML) based reconstruction has been widely investigated and employed in cardiac magnetic resonance (CMR) imaging. ML-based reconstructions can deliver clinically acceptable image quality under substantially accelerated scans. ML-based reconstruction, however, also requires substantial data and computational time to train the neural network, which is often optimized for a fixed acceleration rate or image contrast. In practice, imaging parameters are often tuned to best suit the diagnosis, which may differ from the training data. This can result in degraded image quality, and multiple trained networks are needed to fulfill the clinical demands. In this study, we propose a foundation model that uses adaptive unrolling, channel-shifting, and Pattern and Contrast-Prompt-UNet (PCP-UNet) to tackle the problem. In particular, the undersampled data goes through a different number of unrolled iterations according to its acceleration rate. Channel-shifting improves reconstructed data quality. The PCP-UNet is equipped with an image contrast and sampling pattern prompt. In vivo CMR experiments were performed using mixed combinations of image contrasts, acceleration rates, and (under)sampling patterns. The proposed foundation model has significantly improved image quality for a wide range of CMR protocols and outperforms the conventional ML-based method.

I2I-Mamba: Multi-modal medical image synthesis via selective state space modeling

In recent years, deep learning models comprising transformer components have pushed the performance envelope in medical image synthesis tasks. Contrary to convolutional neural networks (CNNs) that use static, local filters, transformers use self-attention mechanisms to permit adaptive, non-local filtering to sensitively capture long-range context. However, this sensitivity comes at the expense of substantial model complexity, which can compromise learning efficacy particularly on relatively modest-sized imaging datasets. Here, we propose a novel adversarial model for multi-modal medical image synthesis, I2I-Mamba, that leverages selective state space modeling (SSM) to efficiently capture long-range context while maintaining local precision. To do this, I2I-Mamba injects channel-mixed Mamba (cmMamba) blocks in the bottleneck of a convolutional backbone. In cmMamba blocks, SSM layers are used to learn context across the spatial dimension and channel-mixing layers are used to learn context across the channel dimension of feature maps. Comprehensive demonstrations are reported for imputing missing images in multi-contrast MRI and MRI-CT protocols. Our results indicate that I2I-Mamba offers superior performance against state-of-the-art CNN- and transformer-based methods in synthesizing target-modality images.

GRJointNET: Synergistic Completion and Part Segmentation on 3D Incomplete Point Clouds

Segmentation of three-dimensional (3D) point clouds is an important task for autonomous systems. However, success of segmentation algorithms depends greatly on the quality of the underlying point clouds (resolution, completeness etc.). In particular, incomplete point clouds might reduce a downstream model's performance. GRNet is proposed as a novel and recent deep learning solution to complete point clouds, but it is not capable of part segmentation. On the other hand, our proposed solution, GRJointNet, is an architecture that can perform joint completion and segmentation on point clouds as a successor of GRNet. Features extracted for the two tasks are also utilized by each other to increase the overall performance. We evaluated our proposed network on the ShapeNet-Part dataset and compared its performance to GRNet. Our results demonstrate GRJointNet can outperform GRNet on point completion. It should also be noted that GRNet is not capable of segmentation while GRJointNet is. This study1, therefore, holds a promise to enhance practicality and utility of point clouds in 3D vision for autonomous systems.

DDM$^2$: Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models

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 Diffusion Models for Denoising Diffusion MRI (DDM$^2$), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM$^2$ demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

ResViT: Residual vision transformers for multi-modal medical image synthesis

Multi-modal imaging is a key healthcare technology in the diagnosis and management of disease, but it is often underutilized due to costs associated with multiple separate scans. This limitation yields the need for synthesis of unacquired modalities from the subset of available modalities. In recent years, generative adversarial network (GAN) models with superior depiction of structural details have been established as state-of-the-art in numerous medical image synthesis tasks. However, GANs are characteristically based on convolutional neural network (CNN) backbones that perform local processing with compact filters. This inductive bias, in turn, compromises learning of long-range spatial dependencies. While attention maps incorporated in GANs can multiplicatively modulate CNN features to emphasize critical image regions, their capture of global context is mostly implicit. Here, we propose a novel generative adversarial approach for medical image synthesis, ResViT, to combine local precision of convolution operators with contextual sensitivity of vision transformers. Based on an encoder-decoder architecture, ResViT employs a central bottleneck comprising novel aggregated residual transformer (ART) blocks that synergistically combine convolutional and transformer modules. Comprehensive demonstrations are performed for synthesizing missing sequences in multi-contrast MRI and CT images from MRI. Our results indicate the superiority of ResViT against competing methods in terms of qualitative observations and quantitative metrics.

Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers

Supervised deep learning has swiftly become a workhorse for accelerated MRI in recent years, offering state-of-the-art performance in image reconstruction from undersampled acquisitions. Training deep supervised models requires large datasets of undersampled and fully-sampled acquisitions typically from a matching set of subjects. Given scarce access to large medical datasets, this limitation has sparked interest in unsupervised methods that reduce reliance on fully-sampled ground-truth data. A common framework is based on the deep image prior, where network-driven regularization is enforced directly during inference on undersampled acquisitions. Yet, canonical convolutional architectures are suboptimal in capturing long-range relationships, and randomly initialized networks may hamper convergence. To address these limitations, here we introduce a novel unsupervised MRI reconstruction method based on zero-Shot Learned Adversarial TransformERs (SLATER). SLATER embodies a deep adversarial network with cross-attention transformer blocks to map noise and latent variables onto MR images. This unconditional network learns a high-quality MRI prior in a self-supervised encoding task. A zero-shot reconstruction is performed on undersampled test data, where inference is performed by optimizing network parameters, latent and noise variables to ensure maximal consistency to multi-coil MRI data. Comprehensive experiments on brain MRI datasets clearly demonstrate the superior performance of SLATER against several state-of-the-art unsupervised methods.

A Few-Shot Learning Approach for Accelerated MRI via Fusion of Data-Driven and Subject-Driven Priors

Deep neural networks (DNNs) have recently found emerging use in accelerated MRI reconstruction. DNNs typically learn data-driven priors from large datasets constituting pairs of undersampled and fully-sampled acquisitions. Acquiring such large datasets, however, might be impractical. To mitigate this limitation, we propose a few-shot learning approach for accelerated MRI that merges subject-driven priors obtained via physical signal models with data-driven priors obtained from a few training samples. Demonstrations on brain MR images from the NYU fastMRI dataset indicate that the proposed approach requires just a few samples to outperform traditional parallel imaging and DNN algorithms.

Three Dimensional MR Image Synthesis with Progressive Generative Adversarial Networks

Mainstream deep models for three-dimensional MRI synthesis are either cross-sectional or volumetric depending on the input. Cross-sectional models can decrease the model complexity, but they may lead to discontinuity artifacts. On the other hand, volumetric models can alleviate the discontinuity artifacts, but they might suffer from loss of spatial resolution due to increased model complexity coupled with scarce training data. To mitigate the limitations of both approaches, we propose a novel model that progressively recovers the target volume via simpler synthesis tasks across individual orientations.

Progressively Volumetrized Deep Generative Models for Data-Efficient Contextual Learning of MR Image Recovery

Magnetic resonance imaging (MRI) offers the flexibility to image a given anatomic volume under a multitude of tissue contrasts. Yet, scan time considerations put stringent limits on the quality and diversity of MRI data. The gold-standard approach to alleviate this limitation is to recover high-quality images from data undersampled across various dimensions such as the Fourier domain or contrast sets. A central divide among recovery methods is whether the anatomy is processed per volume or per cross-section. Volumetric models offer enhanced capture of global contextual information, but they can suffer from suboptimal learning due to elevated model complexity. Cross-sectional models with lower complexity offer improved learning behavior, yet they ignore contextual information across the longitudinal dimension of the volume. Here, we introduce a novel data-efficient progressively volumetrized generative model (ProvoGAN) that decomposes complex volumetric image recovery tasks into a series of simpler cross-sectional tasks across individual rectilinear dimensions. ProvoGAN effectively captures global context and recovers fine-structural details across all dimensions, while maintaining low model complexity and data-efficiency advantages of cross-sectional models. Comprehensive demonstrations on mainstream MRI reconstruction and synthesis tasks show that ProvoGAN yields superior performance to state-of-the-art volumetric and cross-sectional models.

Semi-Supervised Learning of Mutually Accelerated Multi-Contrast MRI Synthesis without Fully-Sampled Ground-Truths

This study proposes a novel semi-supervised learning framework for mutually accelerated multi-contrast MRI synthesis that recovers high-quality images without demanding large training sets of costly fully-sampled source or ground-truth target images. The proposed method presents a selective loss function expressed only on a subset of the acquired k-space coefficients and further leverages randomized sampling patterns across training subjects to effectively learn relationships among acquired and nonacquired k-space coefficients at all locations. Comprehensive experiments performed on multi-contrast brain images clearly demonstrate that the proposed method maintains equivalent performance to the gold-standard method based on fully-supervised training while alleviating undesirable reliance of the current synthesis methods on large-scale fully-sampled MRI acquisitions.