arXiv subjects

Hairong Zheng

Publications and source records attributed to Hairong Zheng.

At least 55 records · Page 3Linked to original sources

arXiv2024

High-Frequency Space Diffusion Models for Accelerated MRI

Diffusion models with continuous stochastic differential equations (SDEs) have shown superior performances in image generation. It can serve as a deep generative prior to solving the inverse problem in magnetic resonance (MR) reconstruction. However, low-frequency regions of $k$-space data are typically fully sampled in fast MR imaging, while existing diffusion models are performed throughout the entire image or $k$-space, inevitably introducing uncertainty in the reconstruction of low-frequency regions. Additionally, existing diffusion models often demand substantial iterations to converge, resulting in time-consuming reconstructions. To address these challenges, we propose a novel SDE tailored specifically for MR reconstruction with the diffusion process in high-frequency space (referred to as HFS-SDE). This approach ensures determinism in the fully sampled low-frequency regions and accelerates the sampling procedure of reverse diffusion. Experiments conducted on the publicly available fastMRI dataset demonstrate that the proposed HFS-SDE method outperforms traditional parallel imaging methods, supervised deep learning, and existing diffusion models in terms of reconstruction accuracy and stability. The fast convergence properties are also confirmed through theoretical and experimental validation. Our code and weights are available at https://github.com/Aboriginer/HFS-SDE.

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arXiv2023

Improving Medical Report Generation with Adapter Tuning and Knowledge Enhancement in Vision-Language Foundation Models

Medical report generation demands automatic creation of coherent and precise descriptions for medical images. However, the scarcity of labelled medical image-report pairs poses formidable challenges in developing large-scale neural networks capable of harnessing the potential of artificial intelligence, exemplified by large language models. This study builds upon the state-of-the-art vision-language pre-training and fine-tuning approach, BLIP-2, to customize general large-scale foundation models. Integrating adapter tuning and a medical knowledge enhancement loss, our model significantly improves accuracy and coherence. Validation on the dataset of ImageCLEFmedical 2023 demonstrates our model's prowess, achieving the best-averaged results against several state-of-the-art methods. Significant improvements in ROUGE and CIDEr underscore our method's efficacy, highlighting promising outcomes for the rapid medical-domain adaptation of the vision-language foundation models in addressing challenges posed by data scarcity.

cs.CV↗

arXiv2023

Model-driven CT reconstruction algorithm for nano-resolution X-ray phase contrast imaging

The low-density imaging performance of a zone plate based nano-resolution hard X-ray computed tomography (CT) system can be significantly improved by incorporating a grating-based Lau interferometer. Due to the diffraction, however, the acquired nano-resolution phase signal may suffer splitting problem, which impedes the direct reconstruction of phase contrast CT (nPCT) images. To overcome, a new model-driven nPCT image reconstruction algorithm is developed in this study. In it, the diffraction procedure is mathematically modeled into a matrix B, from which the projections without signal splitting can be generated invertedly. Furthermore, a penalized weighed least-square model with total variation (PWLS-TV) is employed to denoise these projections, from which nPCT images with high accuracy are directly reconstructed. Numerical and physical experiments demonstrate that this new algorithm is able to work with phase projections having any splitting distances. Results also reveal that nPCT images with higher signal-to-noise-ratio (SNR) would be reconstructed from projections with larger signal splittings. In conclusion, a novel model-driven nPCT image reconstruction algorithm with high accuracy and robustness is verified for the Lau interferometer based hard X-ray nano-resolution phase contrast imaging.

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arXiv2023

Super resolution dual-layer CBCT imaging with model-guided deep learning

Objective: This study aims at investigating a novel super resolution CBCT imaging technique with the dual-layer flat panel detector (DL-FPD). Approach: In DL-FPD based CBCT imaging, the low-energy and high-energy projections acquired from the top and bottom detector layers contain intrinsically mismatched spatial information, from which super resolution CBCT images can be generated. To explain, a simple mathematical model is established according to the signal formation procedure in DL-FPD. Next, a dedicated recurrent neural network (RNN), named as suRi-Net, is designed by referring to the above imaging model to retrieve the high resolution dual-energy information. Different phantom experiments are conducted to validate the performance of this newly developed super resolution CBCT imaging method. Main Results: Results show that the proposed suRi-Net can retrieve high spatial resolution information accurately from the low-energy and high-energy projections having lower spatial resolution. Quantitatively, the spatial resolution of the reconstructed CBCT images of the top and bottom detector layers is increased by about 45% and 54%, respectively. Significance: In future, suRi-Net provides a new approach to achieve high spatial resolution dual-energy imaging in DL-FPD based CBCT systems.

physics.med-ph↗

arXiv2023

Self-Supervised Federated Learning for Fast MR Imaging

Federated learning (FL) based magnetic resonance (MR) image reconstruction can facilitate learning valuable priors from multi-site institutions without violating patient's privacy for accelerating MR imaging. However, existing methods rely on fully sampled data for collaborative training of the model. The client that only possesses undersampled data can neither participate in FL nor benefit from other clients. Furthermore, heterogeneous data distributions hinder FL from training an effective deep learning reconstruction model and thus cause performance degradation. To address these issues, we propose a Self-Supervised Federated Learning method (SSFedMRI). SSFedMRI explores the physics-based contrastive reconstruction networks in each client to realize cross-site collaborative training in the absence of fully sampled data. Furthermore, a personalized soft update scheme is designed to simultaneously capture the global shared representations among different centers and maintain the specific data distribution of each client. The proposed method is evaluated on four datasets and compared to the latest state-of-the-art approaches. Experimental results demonstrate that SSFedMRI possesses strong capability in reconstructing accurate MR images both visually and quantitatively on both in-distribution and out-of-distribution datasets.

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arXiv2023

Model-based Federated Learning for Accurate MR Image Reconstruction from Undersampled k-space Data

Deep learning-based methods have achieved encouraging performances in the field of magnetic resonance (MR) image reconstruction. Nevertheless, to properly learn a powerful and robust model, these methods generally require large quantities of data, the collection of which from multiple centers may cause ethical and data privacy violation issues. Lately, federated learning has served as a promising solution to exploit multi-center data while getting rid of the data transfer between institutions. However, high heterogeneity exists in the data from different centers, and existing federated learning methods tend to use average aggregation methods to combine the client's information, which limits the performance and generalization capability of the trained models. In this paper, we propose a Model-based Federated learning framework (ModFed). ModFed has three major contributions: 1) Different from the existing data-driven federated learning methods, model-driven neural networks are designed to relieve each client's dependency on large data; 2) An adaptive dynamic aggregation scheme is proposed to address the data heterogeneity issue and improve the generalization capability and robustness the trained neural network models; 3) A spatial Laplacian attention mechanism and a personalized client-side loss regularization are introduced to capture the detailed information for accurate image reconstruction. ModFed is evaluated on three in-vivo datasets. Experimental results show that ModFed has strong capability in improving image reconstruction quality and enforcing model generalization capability when compared to the other five state-of-the-art federated learning approaches. Codes will be made available at https://github.com/ternencewu123/ModFed.

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arXiv2023

Multimodal Brain Disease Classification with Functional Interaction Learning from Single fMRI Volume

In neuroimaging analysis, fMRI can well assess the function changes for brain diseases with no obvious structural lesions. To date, most deep-learning-based fMRI studies have employed functional connectivity (FC) as the basic feature for disease classification. However, FC is calculated on time series of predefined regions of interest and neglects detailed information contained in each voxel. Another drawback of using FC is the limited sample size for the training of deep models. The low representation ability of FC leads to poor performance in clinical practice, especially when dealing with multimodal medical data involving multiple types of visual signals and textual records for brain diseases. To overcome this bottleneck problem in the fMRI feature modality, we propose BrainFormer, an end-to-end functional interaction learning method for brain disease classification with single fMRI volume. Unlike traditional deep learning methods that construct convolution and transformers on FC, BrainFormer learns the functional interaction from fMRI signals, by modeling the local cues within each voxel with 3D convolutions and capturing the global correlations among distant regions with specially designed global attention mechanisms from shallow layers to deep layers. Meanwhile, BrainFormer can deal with multimodal medical data including fMRI volume, structural MRI, FC features and phenotypic data to achieve more comprehensive brain disease diagnosis. We evaluate BrainFormer on five independent multi-site datasets on autism, Alzheimer's disease, depression, attention deficit hyperactivity disorder and headache disorders. The results demonstrate its effectiveness and generalizability for multiple brain diseases diagnosis with multimodal features. BrainFormer may promote precision of neuroimaging-based diagnosis in clinical practice and motivate future studies on fMRI analysis.

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arXiv2022

SPIRiT-Diffusion: SPIRiT-driven Score-Based Generative Modeling for Vessel Wall imaging

Diffusion model is the most advanced method in image generation and has been successfully applied to MRI reconstruction. However, the existing methods do not consider the characteristics of multi-coil acquisition of MRI data. Therefore, we give a new diffusion model, called SPIRiT-Diffusion, based on the SPIRiT iterative reconstruction algorithm. Specifically, SPIRiT-Diffusion characterizes the prior distribution of coil-by-coil images by score matching and characterizes the k-space redundant prior between coils based on self-consistency. With sufficient prior constraint utilized, we achieve superior reconstruction results on the joint Intracranial and Carotid Vessel Wall imaging dataset.

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arXiv2022

Iterative Data Refinement for Self-Supervised MR Image Reconstruction

Magnetic Resonance Imaging (MRI) has become an important technique in the clinic for the visualization, detection, and diagnosis of various diseases. However, one bottleneck limitation of MRI is the relatively slow data acquisition process. Fast MRI based on k-space undersampling and high-quality image reconstruction has been widely utilized, and many deep learning-based methods have been developed in recent years. Although promising results have been achieved, most existing methods require fully-sampled reference data for training the deep learning models. Unfortunately, fully-sampled MRI data are difficult if not impossible to obtain in real-world applications. To address this issue, we propose a data refinement framework for self-supervised MR image reconstruction. Specifically, we first analyze the reason of the performance gap between self-supervised and supervised methods and identify that the bias in the training datasets between the two is one major factor. Then, we design an effective self-supervised training data refinement method to reduce this data bias. With the data refinement, an enhanced self-supervised MR image reconstruction framework is developed to prompt accurate MR imaging. We evaluate our method on an in-vivo MRI dataset. Experimental results show that without utilizing any fully sampled MRI data, our self-supervised framework possesses strong capabilities in capturing image details and structures at high acceleration factors.

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arXiv2022

Uncertainty-Aware Multi-Parametric Magnetic Resonance Image Information Fusion for 3D Object Segmentation

Multi-parametric magnetic resonance (MR) imaging is an indispensable tool in the clinic. Consequently, automatic volume-of-interest segmentation based on multi-parametric MR imaging is crucial for computer-aided disease diagnosis, treatment planning, and prognosis monitoring. Despite the extensive studies conducted in deep learning-based medical image analysis, further investigations are still required to effectively exploit the information provided by different imaging parameters. How to fuse the information is a key question in this field. Here, we propose an uncertainty-aware multi-parametric MR image feature fusion method to fully exploit the information for enhanced 3D image segmentation. Uncertainties in the independent predictions of individual modalities are utilized to guide the fusion of multi-modal image features. Extensive experiments on two datasets, one for brain tissue segmentation and the other for abdominal multi-organ segmentation, have been conducted, and our proposed method achieves better segmentation performance when compared to existing models.

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arXiv2022

Semi-Supervised and Self-Supervised Collaborative Learning for Prostate 3D MR Image Segmentation

Volumetric magnetic resonance (MR) image segmentation plays an important role in many clinical applications. Deep learning (DL) has recently achieved state-of-the-art or even human-level performance on various image segmentation tasks. Nevertheless, manually annotating volumetric MR images for DL model training is labor-exhaustive and time-consuming. In this work, we aim to train a semi-supervised and self-supervised collaborative learning framework for prostate 3D MR image segmentation while using extremely sparse annotations, for which the ground truth annotations are provided for just the central slice of each volumetric MR image. Specifically, semi-supervised learning and self-supervised learning methods are used to generate two independent sets of pseudo labels. These pseudo labels are then fused by Boolean operation to extract a more confident pseudo label set. The images with either manual or network self-generated labels are then employed to train a segmentation model for target volume extraction. Experimental results on a publicly available prostate MR image dataset demonstrate that, while requiring significantly less annotation effort, our framework generates very encouraging segmentation results. The proposed framework is very useful in clinical applications when training data with dense annotations are difficult to obtain.

cs.CV↗

arXiv2022

PARCEL: Physics-based Unsupervised Contrastive Representation Learning for Multi-coil MR Imaging

With the successful application of deep learning to magnetic resonance (MR) imaging, parallel imaging techniques based on neural networks have attracted wide attention. However, in the absence of high-quality, fully sampled datasets for training, the performance of these methods is limited. And the interpretability of models is not strong enough. To tackle this issue, this paper proposes a Physics-bAsed unsupeRvised Contrastive rEpresentation Learning (PARCEL) method to speed up parallel MR imaging. Specifically, PARCEL has a parallel framework to contrastively learn two branches of model-based unrolling networks from augmented undersampled multi-coil k-space data. A sophisticated co-training loss with three essential components has been designed to guide the two networks in capturing the inherent features and representations for MR images. And the final MR image is reconstructed with the trained contrastive networks. PARCEL was evaluated on two vivo datasets and compared to five state-of-the-art methods. The results show that PARCEL is able to learn essential representations for accurate MR reconstruction without relying on fully sampled datasets.

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arXiv2022

Super resolution dual-energy cone-beam CT imaging with dual-layer flat-panel detector

For medical cone-beam computed tomography (CBCT) imaging, the native receptor array of the flat-panel detector (FPD) is usually binned into a reduced matrix size. By doing so, the signal readout speed can be increased by over 4-9 times at the expense of sacrificing the spatial resolution by at least 50%-67%. Clearly, such tradition poses a main bottleneck in generating high spatial resolution and high temporal resolution CBCT images at the same time. In addition, the conventional FPD is also difficult in generating dual-energy CBCT images. In this paper, we propose an innovative super resolution dual-energy CBCT imaging method, named as suRi, based on dual-layer FPD (DL-FPD) to overcome these aforementioned difficulties at once. With suRi, specifically, an 1D or 2D sub-pixel (half pixel in this study) shifted binning is applied to replace the conventionally aligned binning to double the spatial sampling rate during the dual-energy data acquisition. As a result, the suRi approach provides a new strategy to enable high signal readout speed and high spatial resolution CBCT imaging with FPD. Moreover, a penalized likelihood material decomposition algorithm is developed to directly reconstruct the high resolution bases from the dual-energy CBCT projections containing spatial sub-pixel shifts. Experiments based on the single-layer FPD and DL-FPD are performed with physical phantoms and biological specimen to validate this newly developed suRi method. The synthesized monochromatic CT imaging results demonstrate that suRi can significantly improve the spatial image resolution by 46.15%. We believe the developed suRi method would be capable to greatly enhance the imaging performance of the DL-FPD based dual-energy CBCT systems in future.

physics.med-ph↗

arXiv2022

CMOS based high-resolution dynamic X-ray imaging with inorganic perovskite

High-resolution dynamic X-ray detector is crucial for time-resolved digital radiography (DR) imaging and fast 3D medical computed tomography (CT) imaging. Recently, perovskites have become promising alternatives to conventional semi-conductor materials, e.g., Si, a-Se and CdTe, for direct X-ray detection. However, the feasibility of their combination with high-speed pixelated complementary metal-oxide-semiconductor (CMOS) arrays remains unknown. This work originally reports an innovative direct-conversion X-ray detector fabricated with 300 micrometer thick inorganic perovskite film printed on a tailored CMOS array. In-house measurements demonstrate that the CsPbBr3 film has excellent optoelectric properties of an electron mobility-lifetime product of 3.40x10$^{-5}$ cm$^2$ V$^{-1}$, and the X-ray detector exhibits high sensitivity of 9341uC Gy$_{\rm air}^{-1}$ cm$^{-2}$, and low detection limit of 588 nGy$_{\rm air}^{-1}$. This CMOS X-ray imaging detector achieves a high spatial resolution up to 5.5 lp/mm (close to the resolution limit of 6.0 lp/mm), and >300 frame per second (fps) readout speed. DR image of a resolution pattern phantom and a anesthesia mice, CT images of a biological specimen are acquired for the first time.

physics.app-ph↗

arXiv2022

SelfCoLearn: Self-supervised collaborative learning for accelerating dynamic MR imaging

Lately, deep learning has been extensively investigated for accelerating dynamic magnetic resonance (MR) imaging, with encouraging progresses achieved. However, without fully sampled reference data for training, current approaches may have limited abilities in recovering fine details or structures. To address this challenge, this paper proposes a self-supervised collaborative learning framework (SelfCoLearn) for accurate dynamic MR image reconstruction from undersampled k-space data. The proposed framework is equipped with three important components, namely, dual-network collaborative learning, reunderampling data augmentation and a specially designed co-training loss. The framework is flexible to be integrated with both data-driven networks and model-based iterative un-rolled networks. Our method has been evaluated on in-vivo dataset and compared it to four state-of-the-art methods. Results show that our method possesses strong capabilities in capturing essential and inherent representations for direct reconstructions from the undersampled k-space data and thus enables high-quality and fast dynamic MR imaging.

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arXiv2022

Rethinking the optimization process for self-supervised model-driven MRI reconstruction

Recovering high-quality images from undersampled measurements is critical for accelerated MRI reconstruction. Recently, various supervised deep learning-based MRI reconstruction methods have been developed. Despite the achieved promising performances, these methods require fully sampled reference data, the acquisition of which is resource-intensive and time-consuming. Self-supervised learning has emerged as a promising solution to alleviate the reliance on fully sampled datasets. However, existing self-supervised methods suffer from reconstruction errors due to the insufficient constraint enforced on the non-sampled data points and the error accumulation happened alongside the iterative image reconstruction process for model-driven deep learning reconstrutions. To address these challenges, we propose K2Calibrate, a K-space adaptation strategy for self-supervised model-driven MR reconstruction optimization. By iteratively calibrating the learned measurements, K2Calibrate can reduce the network's reconstruction deterioration caused by statistically dependent noise. Extensive experiments have been conducted on the open-source dataset FastMRI, and K2Calibrate achieves better results than five state-of-the-art methods. The proposed K2Calibrate is plug-and-play and can be easily integrated with different model-driven deep learning reconstruction methods.

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arXiv2022

Dual-domain Attention-based Deep Network for Sparse-view CT Artifact Reduction

Due to the wide applications of X-ray computed tomography (CT) in medical imaging activities, radiation exposure has become a major concern for public health. Sparse-view CT is a promising approach to reduce the radiation dose by down-sampling the total number of acquired projections. However, the CT images reconstructed by this sparse-view imaging approach suffer from severe streaking artifacts and structural information loss. In this work, an end-to-end dual-domain attention-based deep network (DDANet) is proposed to solve such an ill-posed CT image reconstruction problem. The image-domain CT image and the projection-domain sinogram are put into the two parallel sub-networks of the DDANet to independently extract the distinct high-level feature maps. In addition, a specified attention module is introduced to fuse the aforementioned dual-domain feature maps to allow complementary optimizations of removing the streaking artifacts and mitigating the loss of structure. Numerical simulations, anthropomorphic thorax phantom and in vivo pre-clinical experiments are conducted to verify the sparse-view CT imaging performance of the DDANet. Results demonstrate that this newly developed approach is able to robustly remove the streaking artifacts while maintaining the fine structures. As a result, the DDANet provides a promising solution in achieving high quality sparse-view CT imaging.

physics.med-ph↗

arXiv2022

Expert Knowledge-guided Geometric Representation Learning for Magnetic Resonance Imaging-based Glioma Grading

Radiomics and deep learning have shown high popularity in automatic glioma grading. Radiomics can extract hand-crafted features that quantitatively describe the expert knowledge of glioma grades, and deep learning is powerful in extracting a large number of high-throughput features that facilitate the final classification. However, the performance of existing methods can still be improved as their complementary strengths have not been sufficiently investigated and integrated. Furthermore, lesion maps are usually needed for the final prediction at the testing phase, which is very troublesome. In this paper, we propose an expert knowledge-guided geometric representation learning (ENROL) framework . Geometric manifolds of hand-crafted features and learned features are constructed to mine the implicit relationship between deep learning and radiomics, and therefore to dig mutual consent and essential representation for the glioma grades. With a specially designed manifold discrepancy measurement, the grading model can exploit the input image data and expert knowledge more effectively in the training phase and get rid of the requirement of lesion segmentation maps at the testing phase. The proposed framework is flexible regarding deep learning architectures to be utilized. Three different architectures have been evaluated and five models have been compared, which show that our framework can always generate promising results.

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