Fang Liu

Wei Peng, Li Feng, Guoying Zhao et al.

The inherent slow imaging speed of Magnetic Resonance Image (MRI) has spurred the development of various acceleration methods, typically through heuristically undersampling the MRI measurement domain known as k-space. Recently, deep neural networks have been applied to reconstruct undersampled k-space data and have shown improved reconstruction performance. While most of these methods focus on designing novel reconstruction networks or new training strategies for a given undersampling pattern, e.g., Cartesian undersampling or Non-Cartesian sampling, to date, there is limited research aiming to learn and optimize k-space sampling strategies using deep neural networks. This work proposes a novel optimization framework to learn k-space sampling trajectories by considering it as an Ordinary Differential Equation (ODE) problem that can be solved using neural ODE. In particular, the sampling of k-space data is framed as a dynamic system, in which neural ODE is formulated to approximate the system with additional constraints on MRI physics. In addition, we have also demonstrated that trajectory optimization and image reconstruction can be learned collaboratively for improved imaging efficiency and reconstruction performance. Experiments were conducted on different in-vivo datasets (e.g., brain and knee images) acquired with different sequences. Initial results have shown that our proposed method can generate better image quality in accelerated MRI than conventional undersampling schemes in Cartesian and Non-Cartesian acquisitions.

Ruimin Feng, Albert Jang, Xingxin He et al.

Purpose: To develop a self-supervised scan-specific deep learning framework for reconstructing accelerated multiparametric quantitative MRI (qMRI). Methods: We propose REFINE-MORE (REference-Free Implicit NEural representation with MOdel REinforcement), combining an implicit neural representation (INR) architecture with a model reinforcement module that incorporates MR physics constraints. The INR component enables informative learning of spatiotemporal correlations to initialize multiparametric quantitative maps, which are then further refined through an unrolled optimization scheme enforcing data consistency. To improve computational efficiency, REFINE-MORE integrates a low-rank adaptation strategy that promotes rapid model convergence. We evaluated REFINE-MORE on accelerated multiparametric quantitative magnetization transfer imaging for simultaneous estimation of free water spin-lattice relaxation, tissue macromolecular proton fraction, and magnetization exchange rate, using both phantom and in vivo brain data. Results: Under 4x and 5x accelerations on in vivo data, REFINE-MORE achieved superior reconstruction quality, demonstrating the lowest normalized root-mean-square error and highest structural similarity index compared to baseline methods and other state-of-the-art model-based and deep learning approaches. Phantom experiments further showed strong agreement with reference values, underscoring the robustness and generalizability of the proposed framework. Additionally, the model adaptation strategy improved reconstruction efficiency by approximately fivefold. Conclusion: REFINE-MORE enables accurate and efficient scan-specific multiparametric qMRI reconstruction, providing a flexible solution for high-dimensional, accelerated qMRI applications.

Liping Zhang, Iris Yuwen Zhou, Sydney B. Montesi et al.

Purpose: To propose a domain-conditioned and temporal-guided diffusion modeling method, termed dynamic Diffusion Modeling (dDiMo), for accelerated dynamic MRI reconstruction, enabling diffusion process to characterize spatiotemporal information for time-resolved multi-coil Cartesian and non-Cartesian data. Methods: The dDiMo framework integrates temporal information from time-resolved dimensions, allowing for the concurrent capture of intra-frame spatial features and inter-frame temporal dynamics in diffusion modeling. It employs additional spatiotemporal ($x$-$t$) and self-consistent frequency-temporal ($k$-$t$) priors to guide the diffusion process. This approach ensures precise temporal alignment and enhances the recovery of fine image details. To facilitate a smooth diffusion process, the nonlinear conjugate gradient algorithm is utilized during the reverse diffusion steps. The proposed model was tested on two types of MRI data: Cartesian-acquired multi-coil cardiac MRI and Golden-Angle-Radial-acquired multi-coil free-breathing lung MRI, across various undersampling rates. Results: dDiMo achieved high-quality reconstructions at various acceleration factors, demonstrating improved temporal alignment and structural recovery compared to other competitive reconstruction methods, both qualitatively and quantitatively. This proposed diffusion framework exhibited robust performance in handling both Cartesian and non-Cartesian acquisitions, effectively reconstructing dynamic datasets in cardiac and lung MRI under different imaging conditions. Conclusion: This study introduces a novel diffusion modeling method for dynamic MRI reconstruction.

Wanyu Bian, Albert Jang, Fang Liu

This study introduces a novel approach for image reconstruction based on a diffusion model conditioned on the native data domain. Our method is applied to multi-coil MRI and quantitative MRI reconstruction, leveraging the domain-conditioned diffusion model within the frequency and parameter domains. The prior MRI physics are used as embeddings in the diffusion model, enforcing data consistency to guide the training and sampling process, characterizing MRI k-space encoding in MRI reconstruction, and leveraging MR signal modeling for qMRI reconstruction. Furthermore, a gradient descent optimization is incorporated into the diffusion steps, enhancing feature learning and improving denoising. The proposed method demonstrates a significant promise, particularly for reconstructing images at high acceleration factors. Notably, it maintains great reconstruction accuracy and efficiency for static and quantitative MRI reconstruction across diverse anatomical structures. Beyond its immediate applications, this method provides potential generalization capability, making it adaptable to inverse problems across various domains.

Gengyan Zhao, Fang Liu, Jonathan A. Oler et al.

Brain extraction or skull stripping of magnetic resonance images (MRI) is an essential step in neuroimaging studies, the accuracy of which can severely affect subsequent image processing procedures. Current automatic brain extraction methods demonstrate good results on human brains, but are often far from satisfactory on nonhuman primates, which are a necessary part of neuroscience research. To overcome the challenges of brain extraction in nonhuman primates, we propose a fully-automated brain extraction pipeline combining deep Bayesian convolutional neural network (CNN) and fully connected three-dimensional (3D) conditional random field (CRF). The deep Bayesian CNN, Bayesian SegNet, is used as the core segmentation engine. As a probabilistic network, it is not only able to perform accurate high-resolution pixel-wise brain segmentation, but also capable of measuring the model uncertainty by Monte Carlo sampling with dropout in the testing stage. Then, fully connected 3D CRF is used to refine the probability result from Bayesian SegNet in the whole 3D context of the brain volume. The proposed method was evaluated with a manually brain-extracted dataset comprising T1w images of 100 nonhuman primates. Our method outperforms six popular publicly available brain extraction packages and three well-established deep learning based methods with a mean Dice coefficient of 0.985 and a mean average symmetric surface distance of 0.220 mm. A better performance against all the compared methods was verified by statistical tests (all p-values<10-4, two-sided, Bonferroni corrected). The maximum uncertainty of the model on nonhuman primate brain extraction has a mean value of 0.116 across all the 100 subjects...

Bochen Guan, Jinnian Zhang, William A. Sethares et al.

The memory consumption of most Convolutional Neural Network (CNN) architectures grows rapidly with increasing depth of the network, which is a major constraint for efficient network training on modern GPUs with limited memory, embedded systems, and mobile devices. Several studies show that the feature maps (as generated after the convolutional layers) are the main bottleneck in this memory problem. Often, these feature maps mimic natural photographs in the sense that their energy is concentrated in the spectral domain. Although embedding CNN architectures in the spectral domain is widely exploited to accelerate the training process, we demonstrate that it is also possible to use the spectral domain to reduce the memory footprint, a method we call Spectral Domain Convolutional Neural Network (SpecNet) that performs both the convolution and the activation operations in the spectral domain. The performance of SpecNet is evaluated on three competitive object recognition benchmark tasks (CIFAR-10, SVHN, and ImageNet), and compared with several state-of-the-art implementations. Overall, SpecNet is able to reduce memory consumption by about 60% without significant loss of performance for all tested networks.

Fang Liu, Lihua Chen, Richard Kijowski et al.

Deep learning holds great promise in the reconstruction of undersampled Magnetic Resonance Imaging (MRI) data, providing new opportunities to escalate the performance of rapid MRI. In existing deep learning-based reconstruction methods, supervised training is performed using artifact-free reference images and their corresponding undersampled pairs. The undersampled images are generated by a fixed undersampling pattern in the training, and the trained network is then applied to reconstruct new images acquired with the same pattern in the inference. While such a training strategy can maintain a favorable reconstruction for a pre-selected undersampling pattern, the robustness of the trained network against any discrepancy of undersampling schemes is typically poor. We developed a novel deep learning-based reconstruction framework called SANTIS for efficient MR image reconstruction with improved robustness against sampling pattern discrepancy. SANTIS uses a data cycle-consistent adversarial network combining efficient end-to-end convolutional neural network mapping, data fidelity enforcement and adversarial training for reconstructing accelerated MR images more faithfully. A training strategy employing sampling augmentation with extensive variation of undersampling patterns was further introduced to promote the robustness of the trained network. Compared to conventional reconstruction and standard deep learning methods, SANTIS achieved consistent better reconstruction performance, with lower errors, greater image sharpness and higher similarity with respect to the reference regardless of the undersampling patterns during inference. This novel concept behind SANTIS can particularly be useful towards improving the robustness of deep learning-based image reconstruction against discrepancy between training and evaluation, which is currently an important but less studied open question.

Fang Liu, Li Feng, Richard Kijowski

Quantitative mapping of magnetic resonance (MR) parameters have been shown as valuable methods for improved assessment of a range of diseases. Due to the need to image an anatomic structure multiple times, parameter mapping usually requires long scan times compared to conventional static imaging. Therefore, accelerated parameter mapping is highly-desirable and remains a topic of great interest in the MR research community. While many recent deep learning methods have focused on highly efficient image reconstruction for conventional static MR imaging, applications of deep learning for dynamic imaging and in particular accelerated parameter mapping have been limited. The purpose of this work was to develop and evaluate a novel deep learning-based reconstruction framework called Model-Augmented Neural neTwork with Incoherent k-space Sampling (MANTIS) for efficient MR parameter mapping. Our approach combines end-to-end CNN mapping with k-space consistency using the concept of cyclic loss to further enforce data and model fidelity. Incoherent k-space sampling is used to improve reconstruction performance. A physical model is incorporated into the proposed framework, so that the parameter maps can be efficiently estimated directly from undersampled images. The performance of MANTIS was demonstrated for the spin-spin relaxation time (T2) mapping of the knee joint. Compared to conventional reconstruction approaches that exploited image sparsity, MANTIS yielded lower errors and higher similarity with respect to the reference in the T2 estimation. Our study demonstrated that the proposed MANTIS framework, with a combination of end-to-end CNN mapping, signal model-augmented data consistency, and incoherent k-space sampling, represents a promising approach for efficient MR parameter mapping. MANTIS can potentially be extended to other types of parameter mapping with appropriate models.