Lixuan Chen

Qing Wu, Lixuan Chen, Ce Wang et al.

Emerging neural reconstruction techniques based on tomography (e.g., NeRF, NeAT, and NeRP) have started showing unique capabilities in medical imaging. In this work, we present a novel Polychromatic neural representation (Polyner) to tackle the challenging problem of CT imaging when metallic implants exist within the human body. CT metal artifacts arise from the drastic variation of metal's attenuation coefficients at various energy levels of the X-ray spectrum, leading to a nonlinear metal effect in CT measurements. Recovering CT images from metal-affected measurements hence poses a complicated nonlinear inverse problem where empirical models adopted in previous metal artifact reduction (MAR) approaches lead to signal loss and strongly aliased reconstructions. Polyner instead models the MAR problem from a nonlinear inverse problem perspective. Specifically, we first derive a polychromatic forward model to accurately simulate the nonlinear CT acquisition process. Then, we incorporate our forward model into the implicit neural representation to accomplish reconstruction. Lastly, we adopt a regularizer to preserve the physical properties of the CT images across different energy levels while effectively constraining the solution space. Our Polyner is an unsupervised method and does not require any external training data. Experimenting with multiple datasets shows that our Polyner achieves comparable or better performance than supervised methods on in-domain datasets while demonstrating significant performance improvements on out-of-domain datasets. To the best of our knowledge, our Polyner is the first unsupervised MAR method that outperforms its supervised counterparts. The code for this work is available at: https://github.com/iwuqing/Polyner.

Lixuan Chen, Zhongnan Liu, Jesse Hamilton et al.

Prospective reconstruction is crucial in many clinical applications such as MRI-guided radiotherapy, which demands accurate image reconstruction and fast motion estimation from currently acquired measurements. However, prospective reconstruction remains challenging due to ultra-sparse sampling and stringent latency requirements. In this work, we propose PDMR, a Prospective Dynamic 3D MRI Reconstruction framework with latent-space motion tracking. Our core idea is to learn an efficient and generalizable latent manifold of motion fields offline, enabling rapid online adaptation for prospective reconstruction. Specifically, we parameterize the deformation vector fields (DVFs) on a low-dimensional manifold, effectively reducing the search space for fast online adaptation, and employ a tri-plane representation to achieve geometry-aware and memory-efficient encoding of 3D motion. Experiments on both XCAT digital phantoms and in-house abdominal MRI datasets demonstrate that PDMR achieves high-fidelity and temporally consistent reconstruction across multiple prospective scenarios (Immediate and After-2min), outperforming state-of-the-art retrospective and online methods. Our results suggest a promising pathway toward ultra-fast, motion-aware prospective MRI reconstruction in clinical practice.

Lixuan Chen, Jiangjie Wu, Qing Wu et al.

Longitudinal fetal brain atlas is a powerful tool for understanding and characterizing the complex process of fetus brain development. Existing fetus brain atlases are typically constructed by averaged brain images on discrete time points independently over time. Due to the differences in onto-genetic trends among samples at different time points, the resulting atlases suffer from temporal inconsistency, which may lead to estimating error of the brain developmental characteristic parameters along the timeline. To this end, we proposed a multi-stage deep-learning framework to tackle the time inconsistency issue as a 4D (3D brain volume + 1D age) image data denoising task. Using implicit neural representation, we construct a continuous and noise-free longitudinal fetus brain atlas as a function of the 4D spatial-temporal coordinate. Experimental results on two public fetal brain atlases (CRL and FBA-Chinese atlases) show that the proposed method can significantly improve the atlas temporal consistency while maintaining good fetus brain structure representation. In addition, the continuous longitudinal fetus brain atlases can also be extensively applied to generate finer 4D atlases in both spatial and temporal resolution.

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.

Xuanyu Tian, Lixuan Chen, Qing Wu et al.

Cardiac magnetic resonance (CMR) imaging is widely used to characterize cardiac morphology and function. To accelerate CMR imaging, various methods have been proposed to recover high-quality spatiotemporal CMR images from highly undersampled k-t space data. However, current CMR reconstruction techniques either fail to achieve satisfactory image quality or are restricted by the scarcity of ground truth data, leading to limited applicability in clinical scenarios. In this work, we proposed MoCo-INR, a new unsupervised method that integrates implicit neural representations (INR) with the conventional motion-compensated (MoCo) framework. Using explicit motion modeling and the continuous prior of INRs, MoCo-INR can produce accurate cardiac motion decomposition and high-quality CMR reconstruction. Furthermore, we introduce a new INR network architecture tailored to the CMR problem, which significantly stabilizes model optimization. Experiments on retrospective (simulated) datasets demonstrate the superiority of MoCo-INR over state-of-the-art methods, achieving fast convergence and fine-detailed reconstructions at ultra-high acceleration factors (e.g., 20x in VISTA sampling). Additionally, evaluations on prospective (real-acquired) free-breathing CMR scans highlight the clinical practicality of MoCo-INR for real-time imaging. Several ablation studies further confirm the effectiveness of the critical components of MoCo-INR.

Xuanyu Tian, Lixuan Chen, Qing Wu et al.

Emerging unsupervised implicit neural representation (INR) methods, such as NeRP, NeAT, and SCOPE, have shown great potential to address sparse-view computed tomography (SVCT) inverse problems. Although these INR-based methods perform well in relatively dense SVCT reconstructions, they struggle to achieve comparable performance to supervised methods in sparser SVCT scenarios. They are prone to being affected by noise, limiting their applicability in real clinical settings. Additionally, current methods have not fully explored the use of image domain priors for solving SVCsT inverse problems. In this work, we demonstrate that imperfect reconstruction results can provide effective image domain priors for INRs to enhance performance. To leverage this, we introduce Self-prior embedding neural representation (Spener), a novel unsupervised method for SVCT reconstruction that integrates iterative reconstruction algorithms. During each iteration, Spener extracts local image prior features from the previous iteration and embeds them to constrain the solution space. Experimental results on multiple CT datasets show that our unsupervised Spener method achieves performance comparable to supervised state-of-the-art (SOTA) methods on in-domain data while outperforming them on out-of-domain datasets. Moreover, Spener significantly improves the performance of INR-based methods in handling SVCT with noisy sinograms. Our code is available at https://github.com/MeijiTian/Spener.

Qing Wu, Xu Guo, Lixuan Chen et al.

X-ray CT often suffers from shadowing and streaking artifacts in the presence of metallic materials, which severely degrade imaging quality. Physically, the linear attenuation coefficients (LACs) of metals vary significantly with X-ray energy, causing a nonlinear beam hardening effect (BHE) in CT measurements. Reconstructing CT images from metal-corrupted measurements consequently becomes a challenging nonlinear inverse problem. Existing state-of-the-art (SOTA) metal artifact reduction (MAR) algorithms rely on supervised learning with numerous paired CT samples. While promising, these supervised methods often assume that the unknown LACs are energy-independent, ignoring the energy-induced BHE, which results in limited generalization. Moreover, the requirement for large datasets also limits their applications in real-world scenarios. In this work, we propose Density neural representation (Diner), a novel unsupervised MAR method. Our key innovation lies in formulating MAR as an energy-independent density reconstruction problem that strictly adheres to the photon-tissue absorption physical model. This model is inherently nonlinear and complex, making it a rarely considered approach in inverse imaging problems. By introducing the water-equivalent tissues approximation and a new polychromatic model to characterize the nonlinear CT acquisition process, we directly learn the neural representation of the density map from raw measurements without using external training data. This energy-independent density reconstruction framework fundamentally resolves the nonlinear BHE, enabling superior MAR performance across a wide range of scanning scenarios. Extensive experiments on both simulated and real-world datasets demonstrate the superiority of our unsupervised Diner over popular supervised methods in terms of MAR performance and robustness.

Jiangjie Wu, Lixuan Chen, Zhenghao Li et al.

High-quality 3D fetal brain MRI reconstruction from motion-corrupted 2D slices is crucial for clinical diagnosis. Reliable slice-to-volume registration (SVR)-based motion correction and super-resolution reconstruction (SRR) methods are essential. Deep learning (DL) has demonstrated potential in enhancing SVR and SRR when compared to conventional methods. However, it requires large-scale external training datasets, which are difficult to obtain for clinical fetal MRI. To address this issue, we propose an unsupervised iterative SVR-SRR framework for isotropic HR volume reconstruction. Specifically, SVR is formulated as a function mapping a 2D slice and a 3D target volume to a rigid transformation matrix, which aligns the slice to the underlying location in the target volume. The function is parameterized by a convolutional neural network, which is trained by minimizing the difference between the volume slicing at the predicted position and the input slice. In SRR, a decoding network embedded within a deep image prior framework is incorporated with a comprehensive image degradation model to produce the high-resolution (HR) volume. The deep image prior framework offers a local consistency prior to guide the reconstruction of HR volumes. By performing a forward degradation model, the HR volume is optimized by minimizing loss between predicted slices and the observed slices. Comprehensive experiments conducted on large-magnitude motion-corrupted simulation data and clinical data demonstrate the superior performance of the proposed framework over state-of-the-art fetal brain reconstruction frameworks.