Mariya Doneva

Ke Wang, Mariya Doneva, Jakob Meineke et al.

Magnetic Resonance Fingerprinting (MRF) is an efficient quantitative MRI technique that can extract important tissue and system parameters such as T1, T2, B0, and B1 from a single scan. This property also makes it attractive for retrospectively synthesizing contrast-weighted images. In general, contrast-weighted images like T1-weighted, T2-weighted, etc., can be synthesized directly from parameter maps through spin-dynamics simulation (i.e., Bloch or Extended Phase Graph models). However, these approaches often exhibit artifacts due to imperfections in the mapping, the sequence modeling, and the data acquisition. Here we propose a supervised learning-based method that directly synthesizes contrast-weighted images from the MRF data without going through the quantitative mapping and spin-dynamics simulation. To implement our direct contrast synthesis (DCS) method, we deploy a conditional Generative Adversarial Network (GAN) framework and propose a multi-branch U-Net as the generator. The input MRF data are used to directly synthesize T1-weighted, T2-weighted, and fluid-attenuated inversion recovery (FLAIR) images through supervised training on paired MRF and target spin echo-based contrast-weighted scans. In-vivo experiments demonstrate excellent image quality compared to simulation-based contrast synthesis and previous DCS methods, both visually as well as by quantitative metrics. We also demonstrate cases where our trained model is able to mitigate in-flow and spiral off-resonance artifacts that are typically seen in MRF reconstructions and thus more faithfully represent conventional spin echo-based contrast-weighted images.

Chinmay Rao, Matthias van Osch, Nicola Pezzotti et al.

Since multiple MRI contrasts of the same anatomy contain redundant information, one contrast can guide the reconstruction of an undersampled subsequent contrast. To this end, several end-to-end learning-based guided reconstruction methods have been proposed. However, a key challenge is the requirement of large paired training datasets comprising raw data and aligned reference images. We propose a modular two-stage approach that does not require any k-space training data, relying solely on image-domain datasets, a large part of which can be unpaired. Additionally, our approach provides an explanatory framework for the multi-contrast problem based on the shared and non-shared generative factors underlying two given contrasts. A content/style model of two-contrast image data is learned from a largely unpaired image-domain dataset and is subsequently applied as a plug-and-play operator in iterative reconstruction. The disentanglement of content and style allows explicit representation of contrast-independent and contrast-specific factors. Consequently, incorporating prior information into the reconstruction reduces to a simple replacement of the aliased content of the reconstruction iterate with high-quality content derived from the reference scan. Combining this component with a data consistency step and introducing a general corrective process for the content yields an iterative scheme. We name this novel approach PnP-CoSMo. Various aspects like interpretability and convergence are explored via simulations. Furthermore, its practicality is demonstrated on the public NYU fastMRI DICOM dataset, showing improved generalizability compared to end-to-end methods, and on two in-house multi-coil raw datasets, offering up to 32.6\% more acceleration over learning-based non-guided reconstruction for a given SSIM.

Donghang Lyu, Chinmay Rao, Marius Staring et al.

Cardiac magnetic resonance imaging (CMR) is vital for diagnosing heart diseases, but long scan time remains a major drawback. To address this, accelerated imaging techniques have been introduced by undersampling k-space, which reduces the quality of the resulting images. Recent deep learning advancements aim to speed up scanning while preserving quality, but adapting to various sampling modes and undersampling factors remains challenging. Therefore, building a universal model is a promising direction. In this work, we introduce UPCMR, a universal unrolled model designed for CMR reconstruction. This model incorporates two kinds of learnable prompts, undersampling-specific prompt and spatial-specific prompt, and integrates them with a UNet structure in each block. Overall, by using the CMRxRecon2024 challenge dataset for training and validation, the UPCMR model highly enhances reconstructed image quality across all random sampling scenarios through an effective training strategy compared to some traditional methods, demonstrating strong adaptability potential for this task.

Donghang Lyu, Marius Staring, Hildo Lamb et al.

In recent years, deep learning has attracted increasing attention in the field of Cardiac MRI (CMR) reconstruction due to its superior performance over traditional methods, particularly in handling higher acceleration factors, highlighting its potential for real-world clinical applications. However, current deep learning methods remain limited in generalizability. CMR scans exhibit wide variability in image contrast, sampling patterns, scanner vendors, anatomical structures, and disease types. Most existing models are designed to handle only a single or narrow subset of these variations, leading to performance degradation when faced with distribution shifts. Therefore, it is beneficial to develop a unified model capable of generalizing across diverse CMR scenarios. To this end, we propose CRUNet-MR-Univ, a foundation model that leverages spatio-temporal correlations and prompt-based priors to effectively handle the full diversity of CMR scans. Our approach consistently outperforms baseline methods across a wide range of settings, highlighting its effectiveness and promise.

Donghang Lyu, Marius Staring, Mariya Doneva et al.

Cardiac Magnetic Resonance (CMR) imaging is a non-invasive method for assessing cardiac structure, function, and blood flow. Cine MRI extends this by capturing heart motion, providing detailed insights into cardiac mechanics. To reduce scan time and breath-hold discomfort, fast acquisition techniques have been utilized at the cost of lowering image quality. Recently, Implicit Neural Representation (INR) methods have shown promise in unsupervised reconstruction by learning coordinate-to-value mappings from undersampled data, enabling high-quality image recovery. However, current existing INR methods primarily focus on using coordinate-based positional embeddings to learn the mapping, while overlooking the feature representations of the target point and its neighboring context. In this work, we propose KP-INR, a dual-branch INR method operating in k-space for cardiac cine MRI reconstruction: one branch processes the positional embedding of k-space coordinates, while the other learns from local multi-scale k-space feature representations at those coordinates. By enabling cross-branch interaction and approximating the target k-space values from both branches, KP-INR can achieve strong performance on challenging Cartesian k-space data. Experiments on the CMRxRecon2024 dataset confirms its improved performance over baseline models and highlights its potential in this field.

Nicola Pezzotti, Sahar Yousefi, Mohamed S. Elmahdy et al.

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 Research and NYU Langone Health. All submissions to the challenge were initially ranked based on similarity with a known groundtruth, after which the top 4 submissions were evaluated radiologically. Our method was evaluated by the fastMRI organizers on an independent challenge dataset. It ranked #1, shared #1, and #3 on respectively the 8x accelerated multi-coil, the 4x multi-coil, and the 4x single-coil track. This demonstrates the superior performance and wide applicability of the method.