Assessment of data consistency through cascades of independently recurrent inference machines for fast and robust accelerated MRI reconstruction

Deep learning for efficient reconstruction of highly accelerated 3D FLAIR MRI in neurological deficits

OBJECTIVE

To compare compressed sensing (CS) and the Cascades of Independently Recurrent Inference Machines (CIRIM) with respect to image quality and reconstruction times when 12-fold accelerated scans of patients with neurological deficits are reconstructed.

MATERIALS AND METHODS

Twelve-fold accelerated 3D T2-FLAIR images were obtained from a cohort of 62 patients with neurological deficits on 3 T MRI. Images were reconstructed offline via CS and the CIRIM. Image quality was assessed in a blinded and randomized manner by two experienced interventional neuroradiologists and one experienced pediatric neuroradiologist on imaging artifacts, perceived spatial resolution (sharpness), anatomic conspicuity, diagnostic confidence, and contrast. The methods were also compared in terms of self-referenced quality metrics, image resolution, patient groups and reconstruction time. In ten scans, the contrast ratio (CR) was determined between lesions and white matter. The effect of acceleration factor was assessed in a publicly available fully sampled dataset, since ground truth data are not available in prospectively accelerated clinical scans. Specifically, 451 FLAIR scans, including scans with white matter lesions, were adopted from the FastMRI database to evaluate structural similarity (SSIM) and the CR of lesions and white matter on ranging acceleration factors from four-fold up to 12-fold.

RESULTS

Interventional neuroradiologists significantly preferred the CIRIM for imaging artifacts, anatomic conspicuity, and contrast. One rater significantly preferred the CIRIM in terms of sharpness and diagnostic confidence. The pediatric neuroradiologist preferred CS for imaging artifacts and sharpness. Compared to CS, the CIRIM reconstructions significantly improved in terms of imaging artifacts and anatomic conspicuity (p < 0.01) for higher resolution scans while yielding a 28% higher SNR (p = 0.001) and a 5.8% lower CR (p = 0.04). There were no differences between patient groups. Additionally, CIRIM was five times faster than CS was. An increasing acceleration factor did not lead to changes in CR (p = 0.92), but led to lower SSIM (p = 0.002).

DISCUSSION

Patients with neurological deficits can undergo MRI at a range of moderate to high acceleration. DL reconstruction outperforms CS in terms of image resolution, efficient denoising with a modest reduction in contrast and reduced reconstruction times.

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

BACKGROUND AND OBJECTIVES

Artificial intelligence (AI) is revolutionizing Magnetic Resonance Imaging (MRI) along the acquisition and processing chain. Advanced AI frameworks have been applied in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. However, existing frameworks are often designed to perform tasks independently of each other or are focused on specific models or single datasets, limiting generalization. This work introduces the Advanced Toolbox for Multitask Medical Imaging Consistency (ATOMMIC), a novel open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using deep learning (DL) models and enables MultiTask Learning (MTL) to perform related tasks in an integrated manner, targeting generalization in the MRI domain.

METHODS

We conducted a comprehensive literature review and analyzed 12,479 GitHub repositories to assess the current landscape of AI frameworks for MRI. Subsequently, we demonstrate how ATOMMIC standardizes workflows and improves data interoperability, enabling effective benchmarking of various DL models across MRI tasks and datasets. To showcase ATOMMIC's capabilities, we evaluated twenty-five DL models on eight publicly available datasets, focusing on accelerated MRI reconstruction, segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and segmentation using MTL.

RESULTS

ATOMMIC's high-performance training and testing capabilities, utilizing multiple GPUs and mixed precision support, enable efficient benchmarking of multiple models across various tasks. The framework's modular architecture implements each task through a collection of data loaders, models, loss functions, evaluation metrics, and pre-processing transformations, facilitating seamless integration of new tasks, datasets, and models. Our findings demonstrate that ATOMMIC supports MTL for multiple MRI tasks with harmonized complex-valued and real-valued data support while maintaining active development and documentation. Task-specific evaluations demonstrate that physics-based models outperform other approaches in reconstructing highly accelerated acquisitions. These high-quality reconstruction models also show superior accuracy in estimating quantitative parameter maps. Furthermore, when combining high-performing reconstruction models with robust segmentation networks through MTL, performance is improved in both tasks.

CONCLUSIONS

ATOMMIC advances MRI reconstruction and analysis by leveraging MTL and ensuring consistency across tasks, models, and datasets. This comprehensive framework serves as a versatile platform for researchers to use existing AI methods and develop new approaches in medical imaging.

Joint reconstruction and segmentation in undersampled 3D knee MRI combining shape knowledge and deep learning

Objective.Task-adapted image reconstruction methods using end-to-end trainable neural networks (NNs) have been proposed to optimize reconstruction for subsequent processing tasks, such as segmentation. However, their training typically requires considerable hardware resources and thus, only relatively simple building blocks, e.g. U-Nets, are typically used, which, albeit powerful, do not integrate model-specific knowledge.Approach.In this work, we extend an end-to-end trainable task-adapted image reconstruction method for a clinically realistic reconstruction and segmentation problem of bone and cartilage in 3D knee MRI by incorporating statistical shape models (SSMs). The SSMs model the prior information and help to regularize the segmentation maps as a final post-processing step. We compare the proposed method to a simultaneous multitask learning approach for image reconstruction and segmentation (MTL) and to a complex SSMs-informed segmentation pipeline (SIS).Main results.Our experiments show that the combination of joint end-to-end training and SSMs to further regularize the segmentation maps obtained by MTL highly improves the results, especially in terms of mean and maximal surface errors. In particular, we achieve the segmentation quality of SIS and, at the same time, a substantial model reduction that yields a five-fold decimation in model parameters and a computational speedup of an order of magnitude.Significance.Remarkably, even for undersampling factors of up toR= 8, the obtained segmentation maps are of comparable quality to those obtained by SIS from ground-truth images.

Dynamic recurrent inference machines for accelerated MRI-guided radiotherapy of the liver

Recurrent inference machines (RIM), a deep learning model that learns an iterative scheme for reconstructing sparsely sampled MRI, has been shown able to perform well on accelerated 2D and 3D MRI scans, learn from small datasets and generalize well to unseen types of data. Here we propose the dynamic recurrent inference machine (DRIM) for reconstructing sparsely sampled 4D MRI by exploiting correlations between respiratory states. The DRIM was applied to a 4D protocol for MR-guided radiotherapy of liver lesions based on repetitive interleaved coronal 2D multi-slice T2-weighted acquisitions. We demonstrate with an ablation study that the DRIM outperforms the RIM, increasing the SSIM score from about 0.89 to 0.95. The DRIM allowed for an approximately 2.7 times faster scan time than the current clinical protocol with only a slight loss in image sharpness. Correlations between slice locations can also be used, but were found to be of less importance, as were a majority of tested variations in network architecture, as long as the respiratory states are processed by the network. Through cross-validation, the DRIM is also shown to be robust in terms of training data. We further demonstrate a good performance across a large range of subsampling factors, and conclude through an evaluation by a radiation oncologist that reconstructed images of the liver contour and inner structures are of a clinically acceptable standard at acceleration factors 10x and 8x, respectively. Finally, we show that binning the data with respect to respiratory states prior to reconstruction comes at a slight cost to reconstruction quality, but at greater speed of the overall protocol.

QOCT-Net: A Physics-Informed Neural Network for Intravascular Optical Coherence Tomography Attenuation Imaging

Intravascular optical coherence tomography (IVOCT) provides high-resolution, depth-resolved images of coronary arterial microstructure by acquiring backscattered light. Quantitative attenuation imaging is important for accurate characterization of tissue components and identification of vulnerable plaques. In this work, we proposed a deep learning method for IVOCT attenuation imaging based on the multiple scattering model of light transport. A physics-informed deep network named Quantitative OCT Network (QOCT-Net) was designed to recover pixel-level optical attenuation coefficients directly from standard IVOCT B-scan images. The network was trained and tested on simulation and in vivo datasets. Results showed superior attenuation coefficient estimates both visually and based on quantitative image metrics. The structural similarity, energy error depth and peak signal-to-noise ratio are improved by at least 7%, 5% and 12.4%, respectively, compared with the state-of-the-art non-learning methods. This method potentially enables high-precision quantitative imaging for tissue characterization and vulnerable plaque identification.

A unified model for reconstruction and R2* mapping of accelerated 7T data using the quantitative recurrent inference machine

Quantitative MRI (qMRI) acquired at the ultra-high field of 7 Tesla has been used in visualizing and analyzing subcortical structures. qMRI relies on the acquisition of multiple images with different scan settings, leading to extended scanning times. Data redundancy and prior information from the relaxometry model can be exploited by deep learning to accelerate the imaging process. We propose the quantitative Recurrent Inference Machine (qRIM), with a unified forward model for joint reconstruction and R₂^*-mapping from sparse data, embedded in a Recurrent Inference Machine (RIM), an iterative inverse problem-solving network. To study the dependency of the proposed extension of the unified forward model to network architecture, we implemented and compared a quantitative End-to-End Variational Network (qE2EVN). Experiments were performed with high-resolution multi-echo gradient echo data of the brain at 7T of a cohort study covering the entire adult life span. The error in reconstructed R₂^* from undersampled data relative to reference data significantly decreased for the unified model compared to sequential image reconstruction and parameter fitting using the RIM. With increasing acceleration factor, an increasing reduction in the reconstruction error was observed, pointing to a larger benefit for sparser data. Qualitatively, this was following an observed reduction of image blurriness in R₂^*-maps. In contrast, when using the U-Net as network architecture, a negative bias in R₂^* in selected regions of interest was observed. Compressed Sensing rendered accurate, but less precise estimates of R₂^*. The qE2EVN showed slightly inferior reconstruction quality compared to the qRIM but better quality than the U-Net and Compressed Sensing. Subcortical maturation over age measured by a linearly increasing interquartile range of R₂^* in the striatum was preserved up to an acceleration factor of 9. With the integrated prior of the unified forward model, the proposed qRIM can exploit the redundancy among repeated measurements and shared information between tasks, facilitating relaxometry in accelerated MRI.