Ruimin Feng

Qing Wu, Ruimin Feng, Hongjiang Wei et al.

In the present work, we propose a Self-supervised COordinate Projection nEtwork (SCOPE) to reconstruct the artifacts-free CT image from a single SV sinogram by solving the inverse tomography imaging problem. Compared with recent related works that solve similar problems using implicit neural representation network (INR), our essential contribution is an effective and simple re-projection strategy that pushes the tomography image reconstruction quality over supervised deep learning CT reconstruction works. The proposed strategy is inspired by the simple relationship between linear algebra and inverse problems. To solve the under-determined linear equation system, we first introduce INR to constrain the solution space via image continuity prior and achieve a rough solution. And secondly, we propose to generate a dense view sinogram that improves the rank of the linear equation system and produces a more stable CT image solution space. Our experiment results demonstrate that the re-projection strategy significantly improves the image reconstruction quality (+3 dB for PSNR at least). Besides, we integrate the recent hash encoding into our SCOPE model, which greatly accelerates the model training. Finally, we evaluate SCOPE in parallel and fan X-ray beam SVCT reconstruction tasks. Experimental results indicate that the proposed SCOPE model outperforms two latest INR-based methods and two well-popular supervised DL methods quantitatively and qualitatively.

Jie Feng, Ruimin Feng, Qing Wu et al.

Supervised Deep-Learning (DL)-based reconstruction algorithms have shown state-of-the-art results for highly-undersampled dynamic Magnetic Resonance Imaging (MRI) reconstruction. However, the requirement of excessive high-quality ground-truth data hinders their applications due to the generalization problem. Recently, Implicit Neural Representation (INR) has appeared as a powerful DL-based tool for solving the inverse problem by characterizing the attributes of a signal as a continuous function of corresponding coordinates in an unsupervised manner. In this work, we proposed an INR-based method to improve dynamic MRI reconstruction from highly undersampled k-space data, which only takes spatiotemporal coordinates as inputs. Specifically, the proposed INR represents the dynamic MRI images as an implicit function and encodes them into neural networks. The weights of the network are learned from sparsely-acquired (k, t)-space data itself only, without external training datasets or prior images. Benefiting from the strong implicit continuity regularization of INR together with explicit regularization for low-rankness and sparsity, our proposed method outperforms the compared scan-specific methods at various acceleration factors. E.g., experiments on retrospective cardiac cine datasets show an improvement of 5.5 ~ 7.1 dB in PSNR for extremely high accelerations (up to 41.6-fold). The high-quality and inner continuity of the images provided by INR has great potential to further improve the spatiotemporal resolution of dynamic MRI, without the need of any training data.

Ruimin Feng, Qing Wu, Jie Feng et al.

Parallel imaging is a commonly used technique to accelerate magnetic resonance imaging (MRI) data acquisition. Mathematically, parallel MRI reconstruction can be formulated as an inverse problem relating the sparsely sampled k-space measurements to the desired MRI image. Despite the success of many existing reconstruction algorithms, it remains a challenge to reliably reconstruct a high-quality image from highly reduced k-space measurements. Recently, implicit neural representation has emerged as a powerful paradigm to exploit the internal information and the physics of partially acquired data to generate the desired object. In this study, we introduced IMJENSE, a scan-specific implicit neural representation-based method for improving parallel MRI reconstruction. Specifically, the underlying MRI image and coil sensitivities were modeled as continuous functions of spatial coordinates, parameterized by neural networks and polynomials, respectively. The weights in the networks and coefficients in the polynomials were simultaneously learned directly from sparsely acquired k-space measurements, without fully sampled ground truth data for training. Benefiting from the powerful continuous representation and joint estimation of the MRI image and coil sensitivities, IMJENSE outperforms conventional image or k-space domain reconstruction algorithms. With extremely limited calibration data, IMJENSE is more stable than supervised calibrationless and calibration-based deep-learning methods. Results show that IMJENSE robustly reconstructs the images acquired at 5$\mathbf{\times}$ and 6$\mathbf{\times}$ accelerations with only 4 or 8 calibration lines in 2D Cartesian acquisitions, corresponding to 22.0% and 19.5% undersampling rates. The high-quality results and scanning specificity make the proposed method hold the potential for further accelerating the data acquisition of parallel MRI.

Ruimin Feng, Qing Wu, Yuyao Zhang et al.

Parallel imaging is a widely-used technique to accelerate magnetic resonance imaging (MRI). However, current methods still perform poorly in reconstructing artifact-free MRI images from highly undersampled k-space data. Recently, implicit neural representation (INR) has emerged as a new deep learning paradigm for learning the internal continuity of an object. In this study, we adopted INR to parallel MRI reconstruction. The MRI image was modeled as a continuous function of spatial coordinates. This function was parameterized by a neural network and learned directly from the measured k-space itself without additional fully sampled high-quality training data. Benefitting from the powerful continuous representations provided by INR, the proposed method outperforms existing methods by suppressing the aliasing artifacts and noise, especially at higher acceleration rates and smaller sizes of the auto-calibration signals. The high-quality results and scanning specificity make the proposed method hold the potential for further accelerating the data acquisition of parallel MRI.

Lixuan Chen, Xuanyu Tian, Jiangjie Wu et al.

Magnetic Resonance Imaging (MRI) stands as a powerful modality in clinical diagnosis. However, it is known that MRI faces challenges such as long acquisition time and vulnerability to motion-induced artifacts. Despite the success of many existing motion correction algorithms, there has been limited research focused on correcting motion artifacts on the estimated coil sensitivity maps for fast MRI reconstruction. Existing methods might suffer from severe performance degradation due to error propagation resulting from the inaccurate coil sensitivity maps estimation. In this work, we propose to jointly estimate the motion parameters and coil sensitivity maps for under-sampled MRI reconstruction, referred to as JSMoCo. However, joint estimation of motion parameters and coil sensitivities results in a highly ill-posed inverse problem due to an increased number of unknowns. To address this, we introduce score-based diffusion models as powerful priors and leverage the MRI physical principles to efficiently constrain the solution space for this optimization problem. Specifically, we parameterize the rigid motion as three trainable variables and model coil sensitivity maps as polynomial functions. Leveraging the physical knowledge, we then employ Gibbs sampler for joint estimation, ensuring system consistency between sensitivity maps and desired images, avoiding error propagation from pre-estimated sensitivity maps to the reconstructed images. We conduct comprehensive experiments to evaluate the performance of JSMoCo on the fastMRI dataset. The results show that our method is capable of reconstructing high-quality MRI images from sparsely-sampled k-space data, even affected by motion. It achieves this by accurately estimating both motion parameters and coil sensitivities, effectively mitigating motion-related challenges during MRI reconstruction.

Ruimin Feng, Xingxin He, Ronald Mercer et al.

Purpose: To investigate whether a vision-language foundation model can enhance undersampled MRI reconstruction by providing high-level contextual information beyond conventional priors. Methods: We proposed a semantic distribution-guided reconstruction framework that uses a pre-trained vision-language foundation model to encode both the reconstructed image and auxiliary information into high-level semantic features. A contrastive objective aligns the reconstructed representation with the target semantic distribution, ensuring consistency with high-level perceptual cues. The proposed objective works with various deep learning-based reconstruction methods and can flexibly incorporate semantic priors from multimodal sources. To test the effectiveness of these semantic priors, we evaluated reconstruction results guided by priors derived from either image-only or image-language auxiliary information. Results: Experiments on knee and brain datasets demonstrate that semantic priors from images preserve fine anatomical structures and achieve superior perceptual quality, as reflected in lower LPIPS values, higher Tenengrad scores, and improved scores in the reader study, compared with conventional regularization. The image-language information further expands the semantic distribution and enables high-level control over reconstruction attributes. Across all evaluations, the contrastive objective consistently guided the reconstructed features toward the desired semantic distributions while maintaining data fidelity, demonstrating the effectiveness of the proposed optimization framework. Conclusion: The study highlights that vision-language foundation models can improve undersampled MRI reconstruction through semantic-space optimization.

Xingxin He, Aurora Rofena, Ruimin Feng et al.

Magnetic Resonance Imaging (MRI) is indispensable in clinical practice but remains constrained by fragmented, multi-stage workflows encompassing acquisition, reconstruction, segmentation, detection, diagnosis, and reporting. While deep learning has achieved progress in individual tasks, existing approaches are often anatomy- or application-specific and lack generalizability across diverse clinical settings. Moreover, current pipelines rarely integrate imaging data with complementary language information that radiologists rely on in routine practice. Here, we introduce OmniMRI, a unified vision-language foundation model designed to generalize across the entire MRI workflow. OmniMRI is trained on a large-scale, heterogeneous corpus curated from 60 public datasets, over 220,000 MRI volumes and 19 million MRI slices, incorporating image-only data, paired vision-text data, and instruction-response data. Its multi-stage training paradigm, comprising self-supervised vision pretraining, vision-language alignment, multimodal pretraining, and multi-task instruction tuning, progressively equips the model with transferable visual representations, cross-modal reasoning, and robust instruction-following capabilities. Qualitative results demonstrate OmniMRI's ability to perform diverse tasks within a single architecture, including MRI reconstruction, anatomical and pathological segmentation, abnormality detection, diagnostic suggestion, and radiology report generation. These findings highlight OmniMRI's potential to consolidate fragmented pipelines into a scalable, generalist framework, paving the way toward foundation models that unify imaging and clinical language for comprehensive, end-to-end MRI interpretation.

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.

Ruimin Feng, Jiayi Zhao, He Wang et al.

Quantitative susceptibility mapping (QSM) has demonstrated great potential in quantifying tissue susceptibility in various brain diseases. However, the intrinsic ill-posed inverse problem relating the tissue phase to the underlying susceptibility distribution affects the accuracy for quantifying tissue susceptibility. Recently, deep learning has shown promising results to improve accuracy by reducing the streaking artifacts. However, there exists a mismatch between the observed phase and the theoretical forward phase estimated by the susceptibility label. In this study, we proposed a model-based deep learning architecture that followed the STI (susceptibility tensor imaging) physical model, referred to as MoDL-QSM. Specifically, MoDL-QSM accounts for the relationship between STI-derived phase contrast induced by the susceptibility tensor terms (ki13,ki23,ki33) and the acquired single-orientation phase. The convolution neural networks are embedded into the physical model to learn a regularization term containing prior information. ki33 and phase induced by ki13 and ki23 terms were used as the labels for network training. Quantitative evaluation metrics (RSME, SSIM, and HFEN) were compared with recently developed deep learning QSM methods. The results showed that MoDL-QSM achieved superior performance, demonstrating its potential for future applications.