arXiv subjects

Shanshan Shan

Publications and source records attributed to Shanshan Shan.

12 recordsLinked to original sources

arXiv2026

SO-Mamba: State-Ownership Mamba for Unrolled MRI Reconstruction

Accelerated MRI reconstruction requires recovering missing details while preserving anatomically coherent structures across large spatial regions. State-space models such as Mamba provide efficient long-range modeling, making them attractive learned regularizers for unrolled reconstruction. However, in a data-consistency-coupled unrolled solver, different stages operate on different reconstruction iterates, where the resident carrier should preserve coherent reconstruction content across stages while stage-dependent non-resident evidence is tied to the current update. Treating these roles uniformly can place persistent resident-carrier evidence and update-dependent non-resident evidence into the same recurrent content route. We therefore propose SO-Mamba, a state-ownership Mamba regularizer that assigns reconstruction evidence within each Mamba stage to recurrent residency, state-interface access, and non-state output correction. SO-Mamba implements this ownership rule with a State-Ownership Router (SOR), which constructs a resident carrier for recurrent content and routes non-resident evidence to affine modulation of the B/C state interfaces and an output correction outlet. The resident carrier supplies the Mamba content route, while the non-resident evidence stream adapts the state interfaces and contributes through the output outlet without entering the recurrent content route. We further introduce a two-level outer-band leakage diagnostic that separates hidden-state storage from readout expression by measuring outer-band energy in the selective-scan state trajectory and the post-scan Mamba readout. Experiments on five public MRI reconstruction benchmarks spanning diverse anatomies, sampling patterns, and coil configurations show that SO-Mamba consistently improves over CNN-, Transformer-, and Mamba-based baselines with competitive computational efficiency.

cs.CV↗

arXiv2025

Two-stage Respiratory Motion-resolved Radial MR Image Reconstruction Using an Interpretable Deep Unrolled Network

Due to the prolonged MRI encoding process, respiratory motion can cause undesired artifacts and image blurring, degrading image quality and limiting clinical applications in abdominal and pulmonary imaging. In this work, we develop a two-stage respiratory motion-resolved radial MR image reconstruction pipeline using an interpretable deep unrolled network (MoraNet), enabling high-quality imaging under free-breathing conditions. Firstly, low-resolution images are reconstructed from the central region of successive golden-angle radial k-space to extract respiratory motion signals. The binned k-space data based on the respiratory signal are then used to reconstruct the motion-resolved high-resolution image for each motion state. The MoraNet applies nonuniform fast Fourier transform (NUFFT) to operate radial encoding and convolutional neural network (CNN) modules to conduct image regularizations. The MoraNet was trained on retrospectively acquired lung MRI images for both fully sampled and undersampled acquisitions. The performance of the proposed method was evaluated on digital CT/MRI breathing XCAT (CoMBAT) phantom data, QUASAR motion phantom data acquired from a 1.0T MRI scanner and volunteer chest data acquired from a 1.5T MRI scanner. The MoraNet pipeline was compared with motion-averaged reconstruction and a conventional compressed sensing (CS)-based method in terms of SSIM, RMSE and computation time. Simulation and experimental results demonstrated that the proposed network could provide accurate respiratory signal estimation and enable effective motion correction. Compared with the CS method, the MoraNet preserved better structural details with lower RMSE and higher SSIM values at acceleration factor of 4, and meanwhile took ten-fold faster inference time.

physics.med-ph↗

arXiv2025

Design and Construction of a Dedicated Radiolucent 8-element Flexible Radiofrequency (RF) Torso Coil for the 1.0T Australian MRI-Linac System

Magnetic resonance imaging-guided linear accelerators (MRI-Linacs) are an emerging treatment technology that enable online soft-tissue visualisation and adaptive radiotherapy. The Australian 1.0 T MRI-Linac employs a fixed, inline beamline, with treatment angles achieved via patient couch rotation, and currently relies on a radiolucent whole-body radiofrequency (RF) coil. However, the large coil-patient separation limits signal-to-noise ratio (SNR) and constrains the fast imaging required for real-time tumour tracking. Here, we show the design and validation of a dedicated, flexible 8-element receive-only RF torso array tailored to the geometry and beam access requirements of the Australian MRI-Linac. Electromagnetic simulations, bench measurements, and phantom imaging demonstrate approximately three-fold SNR improvement at the centre and eight-fold improvement at superficial regions compared with the whole-body coil. In vivo abdominal imaging confirms enhanced anatomical detail and sharper tissue boundaries, and the increased SNR enables parallel imaging with GRAPPA acceleration factors up to three without severe artefacts. Dosimetry measurements and dynamic beam-on noise analysis confirm that the coil array is effectively radiolucent, with dose differences below 1% and no measurable degradation in image noise. This work demonstrates a practical RF solution for accelerated, high-SNR imaging compatible with patient rotation and beam delivery on the Australian MRI-Linac.

physics.med-ph↗

arXiv2025

HiFi-MambaV2: Hierarchical Shared-Routed MoE for High-Fidelity MRI Reconstruction

Reconstructing high-fidelity MR images from undersampled k-space data requires recovering high-frequency details while maintaining anatomical coherence. We present HiFi-MambaV2, a hierarchical shared-routed Mixture-of-Experts (MoE) Mamba architecture that couples frequency decomposition with content-adaptive computation. The model comprises two core components: (i) a separable frequency-consistent Laplacian pyramid (SF-Lap) that delivers alias-resistant, stable low- and high-frequency streams; and (ii) a hierarchical shared-routed MoE that performs per-pixel top-1 sparse dispatch to shared experts and local routers, enabling effective specialization with stable cross-depth behavior. A lightweight global context path is fused into an unrolled, data-consistency-regularized backbone to reinforce long-range reasoning and preserve anatomical coherence. Evaluated on fastMRI, CC359, ACDC, M4Raw, and Prostate158, HiFi-MambaV2 consistently outperforms CNN-, Transformer-, and prior Mamba-based baselines in PSNR, SSIM, and NMSE across single- and multi-coil settings and multiple acceleration factors, consistently surpassing consistent improvements in high-frequency detail and overall structural fidelity. These results demonstrate that HiFi-MambaV2 enables reliable and robust MRI reconstruction.

cs.CV↗

arXiv2025

HiFi-Mamba: Dual-Stream W-Laplacian Enhanced Mamba for High-Fidelity MRI Reconstruction

Reconstructing high-fidelity MR images from undersampled k-space data remains a challenging problem in MRI. While Mamba variants for vision tasks offer promising long-range modeling capabilities with linear-time complexity, their direct application to MRI reconstruction inherits two key limitations: (1) insensitivity to high-frequency anatomical details; and (2) reliance on redundant multi-directional scanning. To address these limitations, we introduce High-Fidelity Mamba (HiFi-Mamba), a novel dual-stream Mamba-based architecture comprising stacked W-Laplacian (WL) and HiFi-Mamba blocks. Specifically, the WL block performs fidelity-preserving spectral decoupling, producing complementary low- and high-frequency streams. This separation enables the HiFi-Mamba block to focus on low-frequency structures, enhancing global feature modeling. Concurrently, the HiFi-Mamba block selectively integrates high-frequency features through adaptive state-space modulation, preserving comprehensive spectral details. To eliminate the scanning redundancy, the HiFi-Mamba block adopts a streamlined unidirectional traversal strategy that preserves long-range modeling capability with improved computational efficiency. Extensive experiments on standard MRI reconstruction benchmarks demonstrate that HiFi-Mamba consistently outperforms state-of-the-art CNN-based, Transformer-based, and other Mamba-based models in reconstruction accuracy while maintaining a compact and efficient model design.

eess.IV↗

arXiv2025

SUSEP-Net: Simulation-Supervised and Contrastive Learning-based Deep Neural Networks for Susceptibility Source Separation

Quantitative susceptibility mapping (QSM) provides a valuable tool for quantifying susceptibility distributions in human brains; however, two types of opposing susceptibility sources (i.e., paramagnetic and diamagnetic), may coexist in a single voxel, and cancel each other out in net QSM images. Susceptibility source separation techniques enable the extraction of sub-voxel information from QSM maps. This study proposes a novel SUSEP-Net for susceptibility source separation by training a dual-branch U-net with a simulation-supervised training strategy. In addition, a contrastive learning framework is included to explicitly impose similarity-based constraints between the branch-specific guidance features in specially-designed encoders and the latent features in the decoders. Comprehensive experiments were carried out on both simulated and in vivo data, including healthy subjects and patients with pathological conditions, to compare SUSEP-Net with three state-of-the-art susceptibility source separation methods (i.e., APART-QSM, \c{hi}-separation, and \c{hi}-sepnet). SUSEP-Net consistently showed improved results compared with the other three methods, with better numerical metrics, improved high-intensity hemorrhage and calcification lesion contrasts, and reduced artifacts in brains with pathological conditions. In addition, experiments on an agarose gel phantom data were conducted to validate the accuracy and the generalization capability of SUSEP-Net.

eess.IV↗

arXiv2025

Highly Undersampled MRI Reconstruction via a Single Posterior Sampling of Diffusion Models

Incoherent k-space undersampling and deep learning-based reconstruction methods have shown great success in accelerating MRI. However, the performance of most previous methods will degrade dramatically under high acceleration factors, e.g., 8$\times$ or higher. Recently, denoising diffusion models (DM) have demonstrated promising results in solving this issue; however, one major drawback of the DM methods is the long inference time due to a dramatic number of iterative reverse posterior sampling steps. In this work, a Single Step Diffusion Model-based reconstruction framework, namely SSDM-MRI, is proposed for restoring MRI images from highly undersampled k-space. The proposed method achieves one-step reconstruction by first training a conditional DM and then iteratively distilling this model four times using an iterative selective distillation algorithm, which works synergistically with a shortcut reverse sampling strategy for model inference. Comprehensive experiments were carried out on both publicly available fastMRI brain and knee images, as well as an in-house multi-echo GRE (QSM) subject. Overall, the results showed that SSDM-MRI outperformed other methods in terms of numerical metrics (e.g., PSNR and SSIM), error maps, image fine details, and latent susceptibility information hidden in MRI phase images. In addition, the reconstruction time for a 320$\times$320 brain slice of SSDM-MRI is only 0.45 second, which is only comparable to that of a simple U-net, making it a highly effective solution for MRI reconstruction tasks.

eess.IV↗

arXiv2024

Accelerating Low-field MRI: From Compressed Sensing to Deep Learning Reconstruction with CNNs and Transformers

Portable, low-field Magnetic Resonance Imaging (MRI) scanners are increasingly being deployed in clinical settings. However, key barriers to their widespread use include low signal-to-noise ratio (SNR), generally low image quality, and long scan durations. Hence, methods for accelerating acquisition and boosting image quality are critically important to enable clinically actionable, high-quality imaging in these systems. Despite the role that compressed sensing (CS) and deep learning (DL)-based methods have played in improving image quality for high-field MRI, their adoption for low-field imaging is still in its infancy, and it remains unclear how robust these methods are in low-SNR regimes. Here, we propose, investigate, and compare four reconstruction approaches: (i) L1-wavelet CS; (ii) a data-driven network; (iii) an unrolled network; and (iv) a Swin Transformer Cascade. We evaluate their performance across a range of SNR values using publicly available datasets and ultra-low field (6.5 mT) MRI data. Our results show that the unrolled network and Swin Transformer cascade outperform CS and data-driven models. While transformer-based models achieve the highest performance at high SNR, unrolled convolution-based networks are more robust in ultra-low SNR settings and often outperform transformers, indicating that simpler DL architectures may be better suited to low-field MRI. This work highlights both the potential and limitations of advanced reconstruction techniques in low-field MRI and pinpoints effective DL strategies for addressing SNR challenges.

physics.med-ph↗

arXiv2024

IR2QSM: Quantitative Susceptibility Mapping via Deep Neural Networks with Iterative Reverse Concatenations and Recurrent Modules

Quantitative susceptibility mapping (QSM) is an MRI phase-based post-processing technique to extract the distribution of tissue susceptibilities, demonstrating significant potential in studying neurological diseases. However, the ill-conditioned nature of dipole inversion makes QSM reconstruction from the tissue field prone to noise and artifacts. In this work, we propose a novel deep learning-based IR2QSM method for QSM reconstruction. It is designed by iterating four times of a reverse concatenations and middle recurrent modules enhanced U-net, which could dramatically improve the efficiency of latent feature utilization. Simulated and in vivo experiments were conducted to compare IR2QSM with several traditional algorithms (MEDI and iLSQR) and state-of-the-art deep learning methods (U-net, xQSM, and LPCNN). The results indicated that IR2QSM was able to obtain QSM images with significantly increased accuracy and mitigated artifacts over other methods. Particularly, IR2QSM demonstrated on average the best NRMSE (27.59%) in simulated experiments, which is 15.48%, 7.86%, 17.24%, 9.26%, and 29.13% lower than iLSQR, MEDI, U-net, xQSM, LPCNN, respectively, and led to improved QSM results with fewer artifacts for the in vivo data.

eess.IV↗

arXiv2024

Image Reconstruction with B0 Inhomogeneity using an Interpretable Deep Unrolled Network on an Open-bore MRI-Linac

MRI-Linac systems require fast image reconstruction with high geometric fidelity to localize and track tumours for radiotherapy treatments. However, B0 field inhomogeneity distortions and slow MR acquisition potentially limit the quality of the image guidance and tumour treatments. In this study, we develop an interpretable unrolled network, referred to as RebinNet, to reconstruct distortion-free images from B0 inhomogeneity-corrupted k-space for fast MRI-guided radiotherapy applications. RebinNet includes convolutional neural network (CNN) blocks to perform image regularizations and nonuniform fast Fourier Transform (NUFFT) modules to incorporate B0 inhomogeneity information. The RebinNet was trained on a publicly available MR dataset from eleven healthy volunteers for both fully sampled and subsampled acquisitions. Grid phantom and human brain images acquired from an open-bore 1T MRI-Linac scanner were used to evaluate the performance of the proposed network. The RebinNet was compared with the conventional regularization algorithm and our recently developed UnUNet method in terms of root mean squared error (RMSE), structural similarity (SSIM), residual distortions, and computation time. Imaging results demonstrated that the RebinNet reconstructed images with lowest RMSE (<0.05) and highest SSIM (>0.92) at four-time acceleration for simulated brain images. The RebinNet could better preserve structural details and substantially improve the computational efficiency (ten-fold faster) compared to the conventional regularization methods, and had better generalization ability than the UnUNet method. The proposed RebinNet can achieve rapid image reconstruction and overcome the B0 inhomogeneity distortions simultaneously, which would facilitate accurate and fast image guidance in radiotherapy treatments.

physics.med-ph↗

arXiv2024

Plug-and-Play Latent Feature Editing for Orientation-Adaptive Quantitative Susceptibility Mapping Neural Networks

Quantitative susceptibility mapping (QSM) is a post-processing technique for deriving tissue magnetic susceptibility distribution from MRI phase measurements. Deep learning (DL) algorithms hold great potential for solving the ill-posed QSM reconstruction problem. However, a significant challenge facing current DL-QSM approaches is their limited adaptability to magnetic dipole field orientation variations during training and testing. In this work, we propose a novel Orientation-Adaptive Latent Feature Editing (OA-LFE) module to learn the encoding of acquisition orientation vectors and seamlessly integrate them into the latent features of deep networks. Importantly, it can be directly Plug-and-Play (PnP) into various existing DL-QSM architectures, enabling reconstructions of QSM from arbitrary magnetic dipole orientations. Its effectiveness is demonstrated by combining the OA-LFE module into our previously proposed phase-to-susceptibility single-step instant QSM (iQSM) network, which was initially tailored for pure-axial acquisitions. The proposed OA-LFE-empowered iQSM, which we refer to as iQSM+, is trained in a self-supervised manner on a specially-designed simulation brain dataset. Comprehensive experiments are conducted on simulated and in vivo human brain datasets, encompassing subjects ranging from healthy individuals to those with pathological conditions. These experiments involve various MRI platforms (3T and 7T) and aim to compare our proposed iQSM+ against several established QSM reconstruction frameworks, including the original iQSM. The iQSM+ yields QSM images with significantly improved accuracies and mitigates artifacts, surpassing other state-of-the-art DL-QSM algorithms.

eess.IV↗

arXiv2023

Distortion-Corrected Image Reconstruction with Deep Learning on an MRI-Linac

Magnetic resonance imaging (MRI) is increasingly utilized for image-guided radiotherapy due to its outstanding soft-tissue contrast and lack of ionizing radiation. However, geometric distortions caused by gradient nonlinearity (GNL) limit anatomical accuracy, potentially compromising the quality of tumour treatments. In addition, slow MR acquisition and reconstruction limit the potential for real-time image guidance. Here, we demonstrate a deep learning-based method that rapidly reconstructs distortion-corrected images from raw k-space data for real-time MR-guided radiotherapy applications. We leverage recent advances in interpretable unrolling networks to develop a Distortion-Corrected Reconstruction Network (DCReconNet) that applies convolutional neural networks (CNNs) to learn effective regularizations and nonuniform fast Fourier transforms for GNL-encoding. DCReconNet was trained on a public MR brain dataset from eleven healthy volunteers for fully sampled and accelerated techniques including parallel imaging (PI) and compressed sensing (CS). The performance of DCReconNet was tested on phantom and volunteer brain data acquired on a 1.0T MRI-Linac. The DCReconNet, CS- and PI-based reconstructed image quality was measured by structural similarity (SSIM) and root-mean-squared error (RMSE) for numerical comparisons. The computation time for each method was also reported. Phantom and volunteer results demonstrated that DCReconNet better preserves image structure when compared to CS- and PI-based reconstruction methods. DCReconNet resulted in highest SSIM (0.95 median value) and lowest RMSE (<0.04) on simulated brain images with four times acceleration. DCReconNet is over 100-times faster than iterative, regularized reconstruction methods. DCReconNet provides fast and geometrically accurate image reconstruction and has potential for real-time MRI-guided radiotherapy applications.

physics.med-ph↗