arXiv subjects

Yanjie Zhu

Publications and source records attributed to Yanjie Zhu.

At least 37 records · Page 2Linked to original sources

arXiv2024

SPIRiT-Diffusion: Self-Consistency Driven Diffusion Model for Accelerated MRI

Diffusion models have emerged as a leading methodology for image generation and have proven successful in the realm of magnetic resonance imaging (MRI) reconstruction. However, existing reconstruction methods based on diffusion models are primarily formulated in the image domain, making the reconstruction quality susceptible to inaccuracies in coil sensitivity maps (CSMs). k-space interpolation methods can effectively address this issue but conventional diffusion models are not readily applicable in k-space interpolation. To overcome this challenge, we introduce a novel approach called SPIRiT-Diffusion, which is a diffusion model for k-space interpolation inspired by the iterative self-consistent SPIRiT method. Specifically, we utilize the iterative solver of the self-consistent term (i.e., k-space physical prior) in SPIRiT to formulate a novel stochastic differential equation (SDE) governing the diffusion process. Subsequently, k-space data can be interpolated by executing the diffusion process. This innovative approach highlights the optimization model's role in designing the SDE in diffusion models, enabling the diffusion process to align closely with the physics inherent in the optimization model, a concept referred to as model-driven diffusion. We evaluated the proposed SPIRiT-Diffusion method using a 3D joint intracranial and carotid vessel wall imaging dataset. The results convincingly demonstrate its superiority over image-domain reconstruction methods, achieving high reconstruction quality even at a substantial acceleration rate of 10.

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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

A Two-Stage Generative Model with CycleGAN and Joint Diffusion for MRI-based Brain Tumor Detection

Accurate detection and segmentation of brain tumors is critical for medical diagnosis. However, current supervised learning methods require extensively annotated images and the state-of-the-art generative models used in unsupervised methods often have limitations in covering the whole data distribution. In this paper, we propose a novel framework Two-Stage Generative Model (TSGM) that combines Cycle Generative Adversarial Network (CycleGAN) and Variance Exploding stochastic differential equation using joint probability (VE-JP) to improve brain tumor detection and segmentation. The CycleGAN is trained on unpaired data to generate abnormal images from healthy images as data prior. Then VE-JP is implemented to reconstruct healthy images using synthetic paired abnormal images as a guide, which alters only pathological regions but not regions of healthy. Notably, our method directly learned the joint probability distribution for conditional generation. The residual between input and reconstructed images suggests the abnormalities and a thresholding method is subsequently applied to obtain segmentation results. Furthermore, the multimodal results are weighted with different weights to improve the segmentation accuracy further. We validated our method on three datasets, and compared with other unsupervised methods for anomaly detection and segmentation. The DSC score of 0.8590 in BraTs2020 dataset, 0.6226 in ITCS dataset and 0.7403 in In-house dataset show that our method achieves better segmentation performance and has better generalization.

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arXiv2023

Physics-Informed DeepMRI: Bridging the Gap from Heat Diffusion to k-Space Interpolation

In the field of parallel imaging (PI), alongside image-domain regularization methods, substantial research has been dedicated to exploring $k$-space interpolation. However, the interpretability of these methods remains an unresolved issue. Furthermore, these approaches currently face acceleration limitations that are comparable to those experienced by image-domain methods. In order to enhance interpretability and overcome the acceleration limitations, this paper introduces an interpretable framework that unifies both $k$-space interpolation techniques and image-domain methods, grounded in the physical principles of heat diffusion equations. Building upon this foundational framework, a novel $k$-space interpolation method is proposed. Specifically, we model the process of high-frequency information attenuation in $k$-space as a heat diffusion equation, while the effort to reconstruct high-frequency information from low-frequency regions can be conceptualized as a reverse heat equation. However, solving the reverse heat equation poses a challenging inverse problem. To tackle this challenge, we modify the heat equation to align with the principles of magnetic resonance PI physics and employ the score-based generative method to precisely execute the modified reverse heat diffusion. Finally, experimental validation conducted on publicly available datasets demonstrates the superiority of the proposed approach over traditional $k$-space interpolation methods, deep learning-based $k$-space interpolation methods, and conventional diffusion models in terms of reconstruction accuracy, particularly in high-frequency regions.

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arXiv2023

Dynamic Dual-Graph Fusion Convolutional Network For Alzheimer's Disease Diagnosis

In this paper, a dynamic dual-graph fusion convolutional network is proposed to improve Alzheimer's disease (AD) diagnosis performance. The following are the paper's main contributions: (a) propose a novel dynamic GCN architecture, which is an end-to-end pipeline for diagnosis of the AD task; (b) the proposed architecture can dynamically adjust the graph structure for GCN to produce better diagnosis outcomes by learning the optimal underlying latent graph; (c) incorporate feature graph learning and dynamic graph learning, giving those useful features of subjects more weight while decreasing the weights of other noise features. Experiments indicate that our model provides flexibility and stability while achieving excellent classification results in AD diagnosis.

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arXiv2023

Meta-Learning Enabled Score-Based Generative Model for 1.5T-Like Image Reconstruction from 0.5T MRI

Magnetic resonance imaging (MRI) is known to have reduced signal-to-noise ratios (SNR) at lower field strengths, leading to signal degradation when producing a low-field MRI image from a high-field one. Therefore, reconstructing a high-field-like image from a low-field MRI is a complex problem due to the ill-posed nature of the task. Additionally, obtaining paired low-field and high-field MR images is often not practical. We theoretically uncovered that the combination of these challenges renders conventional deep learning methods that directly learn the mapping from a low-field MR image to a high-field MR image unsuitable. To overcome these challenges, we introduce a novel meta-learning approach that employs a teacher-student mechanism. Firstly, an optimal-transport-driven teacher learns the degradation process from high-field to low-field MR images and generates pseudo-paired high-field and low-field MRI images. Then, a score-based student solves the inverse problem of reconstructing a high-field-like MR image from a low-field MRI within the framework of iterative regularization, by learning the joint distribution of pseudo-paired images to act as a regularizer. Experimental results on real low-field MRI data demonstrate that our proposed method outperforms state-of-the-art unpaired learning methods.

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arXiv2023

Brain PET Synthesis from MRI Using Joint Probability Distribution of Diffusion Model at Ultrahigh Fields

MRI and PET are important modalities and can provide complementary information for the diagnosis of brain diseases because MRI can provide structural information of brain and PET can obtain functional information of brain. However, PET is usually missing. Especially, simultaneous PET and MRI imaging at ultrahigh field is not achievable in the current. Thus, synthetic PET using MRI at ultrahigh field is essential. In this paper, we synthetic PET using MRI as a guide by joint probability distribution of diffusion model (JPDDM). Meanwhile, We utilized our model in Ultrahigh Fields.

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arXiv2023

Accelerating Magnetic Resonance T1\r{ho} Mapping Using Simultaneously Spatial Patch-based and Parametric Group-based Low-rank Tensors (SMART)

Quantitative magnetic resonance (MR) T1\r{ho} mapping is a promising approach for characterizing intrinsic tissue-dependent information. However, long scan time significantly hinders its widespread applications. Recently, low-rank tensor has been employed and demonstrated good performance in accelerating MR T1\r{ho} mapping. In this study, we propose a novel method that uses spatial patch-based and parametric group-based low rank tensors simultaneously (SMART) to reconstruct images from highly undersampled k-space data. The spatial patch-based low-rank tensor exploits the high local and nonlocal redundancies and similarities between the contrast images in T1\r{ho} mapping. The parametric group based low-rank tensor, which integrates similar exponential behavior of the image signals, is jointly used to enforce the multidimensional low-rankness in the reconstruction process. In vivo brain datasets were used to demonstrate the validity of the proposed method. Experimental results have demonstrated that the proposed method achieves 11.7-fold and 13.21-fold accelerations in two-dimensional and three-dimensional acquisitions, respectively, with more accurate reconstructed images and maps than several state-of-the-art methods. Prospective reconstruction results further demonstrate the capability of the SMART method in accelerating MR T1\r{ho} imaging.

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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

Self-Score: Self-Supervised Learning on Score-Based Models for MRI Reconstruction

Recently, score-based diffusion models have shown satisfactory performance in MRI reconstruction. Most of these methods require a large amount of fully sampled MRI data as a training set, which, sometimes, is difficult to acquire in practice. This paper proposes a fully-sampled-data-free score-based diffusion model for MRI reconstruction, which learns the fully sampled MR image prior in a self-supervised manner on undersampled data. Specifically, we first infer the fully sampled MR image distribution from the undersampled data by Bayesian deep learning, then perturb the data distribution and approximate their probability density gradient by training a score function. Leveraging the learned score function as a prior, we can reconstruct the MR image by performing conditioned Langevin Markov chain Monte Carlo (MCMC) sampling. Experiments on the public dataset show that the proposed method outperforms existing self-supervised MRI reconstruction methods and achieves comparable performances with the conventional (fully sampled data trained) score-based diffusion methods.

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arXiv2022

K-UNN: k-Space Interpolation With Untrained Neural Network

Recently, untrained neural networks (UNNs) have shown satisfactory performances for MR image reconstruction on random sampling trajectories without using additional full-sampled training data. However, the existing UNN-based approach does not fully use the MR image physical priors, resulting in poor performance in some common scenarios (e.g., partial Fourier, regular sampling, etc.) and the lack of theoretical guarantees for reconstruction accuracy. To bridge this gap, we propose a safeguarded k-space interpolation method for MRI using a specially designed UNN with a tripled architecture driven by three physical priors of the MR images (or k-space data), including sparsity, coil sensitivity smoothness, and phase smoothness. We also prove that the proposed method guarantees tight bounds for interpolated k-space data accuracy. Finally, ablation experiments show that the proposed method can more accurately characterize the physical priors of MR images than existing traditional methods. Additionally, under a series of commonly used sampling trajectories, experiments also show that the proposed method consistently outperforms traditional parallel imaging methods and existing UNNs, and even outperforms the state-of-the-art supervised-trained k-space deep learning methods in some cases.

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arXiv2022

PS-Net: Learned Partially Separable Model for Dynamic MR Imaging

Deep learning methods driven by the low-rank regularization have achieved attractive performance in dynamic magnetic resonance (MR) imaging. However, most of these methods represent low-rank prior by hand-crafted nuclear norm, which cannot accurately approximate the low-rank prior over the entire dataset through a fixed regularization parameter. In this paper, we propose a learned low-rank method for dynamic MR imaging. In particular, we unrolled the semi-quadratic splitting method (HQS) algorithm for the partially separable (PS) model to a network, in which the low-rank is adaptively characterized by a learnable null-space transform. Experiments on the cardiac cine dataset show that the proposed model outperforms the state-of-the-art compressed sensing (CS) methods and existing deep learning methods both quantitatively and qualitatively.

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arXiv2021

Equilibrated Zeroth-Order Unrolled Deep Networks for Accelerated MRI

Recently, model-driven deep learning unrolls a certain iterative algorithm of a regularization model into a cascade network by replacing the first-order information (i.e., (sub)gradient or proximal operator) of the regularizer with a network module, which appears more explainable and predictable compared to common data-driven networks. Conversely, in theory, there is not necessarily such a functional regularizer whose first-order information matches the replaced network module, which means the network output may not be covered by the original regularization model. Moreover, up to now, there is also no theory to guarantee the global convergence and robustness (regularity) of unrolled networks under realistic assumptions. To bridge this gap, this paper propose to present a safeguarded methodology on network unrolling. Specifically, focusing on accelerated MRI, we unroll a zeroth-order algorithm, of which the network module represents the regularizer itself, so that the network output can be still covered by the regularization model. Furthermore, inspired by the ideal of deep equilibrium models, before backpropagating, we carry out the unrolled iterative network to converge to a fixed point to ensure the convergence. In case the measurement data contains noise, we prove that the proposed network is robust against noisy interference. Finally, numerical experiments show that the proposed network consistently outperforms the state-of-the-art MRI reconstruction methods including traditional regularization methods and other deep learning methods.

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arXiv2021

Highly accelerated MR parametric mapping by undersampling the k-space and reducing the contrast number simultaneously with deep learning

Purpose: To propose a novel deep learning-based method called RG-Net (reconstruction and generation network) for highly accelerated MR parametric mapping by undersampling k-space and reducing the acquired contrast number simultaneously. Methods: The proposed framework consists of a reconstruction module and a generative module. The reconstruction module reconstructs MR images from the acquired few undersampled k-space data with the help of a data prior. The generative module then synthesizes the remaining multi-contrast images from the reconstructed images, where the exponential model is implicitly incorporated into the image generation through the supervision of fully sampled labels. The RG-Net was evaluated on the T1\r{ho} mapping data of knee and brain at different acceleration rates. Regional T1\r{ho} analysis for cartilage and the brain was performed to access the performance of RG-Net. Results: RG-Net yields a high-quality T1\r{ho} map at a high acceleration rate of 17. Compared with the competing methods that only undersample k-space, our framework achieves better performance in T1\r{ho} value analysis. Our method also improves quality of T1\r{ho} maps on patient with glioma. Conclusion: The proposed RG-Net that adopted a new strategy by undersampling k-space and reducing the contrast number simultaneously for fast MR parametric mapping, can achieve a high acceleration rate while maintaining good reconstruction quality. The generative module of our framework can also be used as an insert module in other fast MR parametric mapping methods. Keywords: Deep learning, convolutional neural network, fast MR parametric mapping

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arXiv2021

Deep Low-rank plus Sparse Network for Dynamic MR Imaging

In dynamic magnetic resonance (MR) imaging, low-rank plus sparse (L+S) decomposition, or robust principal component analysis (PCA), has achieved stunning performance. However, the selection of the parameters of L+S is empirical, and the acceleration rate is limited, which are common failings of iterative compressed sensing MR imaging (CS-MRI) reconstruction methods. Many deep learning approaches have been proposed to address these issues, but few of them use a low-rank prior. In this paper, a model-based low-rank plus sparse network, dubbed L+S-Net, is proposed for dynamic MR reconstruction. In particular, we use an alternating linearized minimization method to solve the optimization problem with low-rank and sparse regularization. Learned soft singular value thresholding is introduced to ensure the clear separation of the L component and S component. Then, the iterative steps are unrolled into a network in which the regularization parameters are learnable. We prove that the proposed L+S-Net achieves global convergence under two standard assumptions. Experiments on retrospective and prospective cardiac cine datasets show that the proposed model outperforms state-of-the-art CS and existing deep learning methods and has great potential for extremely high acceleration factors (up to 24x).

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arXiv2021

SRR-Net: A Super-Resolution-Involved Reconstruction Method for High Resolution MR Imaging

Improving the image resolution and acquisition speed of magnetic resonance imaging (MRI) is a challenging problem. There are mainly two strategies dealing with the speed-resolution trade-off: (1) $k$-space undersampling with high-resolution acquisition, and (2) a pipeline of lower resolution image reconstruction and image super-resolution. However, these approaches either have limited performance at certain high acceleration factor or suffer from the error accumulation of two-step structure. In this paper, we combine the idea of MR reconstruction and image super-resolution, and work on recovering HR images from low-resolution under-sampled $k$-space data directly. Particularly, the SR-involved reconstruction can be formulated as a variational problem, and a learnable network unrolled from its solution algorithm is proposed. A discriminator was introduced to enhance the detail refining performance. Experiment results using in-vivo HR multi-coil brain data indicate that the proposed SRR-Net is capable of recovering high-resolution brain images with both good visual quality and perceptual quality.

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arXiv2021

Deep Manifold Learning for Dynamic MR Imaging

Purpose: To develop a deep learning method on a nonlinear manifold to explore the temporal redundancy of dynamic signals to reconstruct cardiac MRI data from highly undersampled measurements. Methods: Cardiac MR image reconstruction is modeled as general compressed sensing (CS) based optimization on a low-rank tensor manifold. The nonlinear manifold is designed to characterize the temporal correlation of dynamic signals. Iterative procedures can be obtained by solving the optimization model on the manifold, including gradient calculation, projection of the gradient to tangent space, and retraction of the tangent space to the manifold. The iterative procedures on the manifold are unrolled to a neural network, dubbed as Manifold-Net. The Manifold-Net is trained using in vivo data with a retrospective electrocardiogram (ECG)-gated segmented bSSFP sequence. Results: Experimental results at high accelerations demonstrate that the proposed method can obtain improved reconstruction compared with a compressed sensing (CS) method k-t SLR and two state-of-the-art deep learning-based methods, DC-CNN and CRNN. Conclusion: This work represents the first study unrolling the optimization on manifolds into neural networks. Specifically, the designed low-rank manifold provides a new technical route for applying low-rank priors in dynamic MR imaging.

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arXiv2020

Is Each Layer Non-trivial in CNN?

Convolutional neural network (CNN) models have achieved great success in many fields. With the advent of ResNet, networks used in practice are getting deeper and wider. However, is each layer non-trivial in networks? To answer this question, we trained a network on the training set, then we replace the network convolution kernels with zeros and test the result models on the test set. We compared experimental results with baseline and showed that we can reach similar or even the same performances. Although convolution kernels are the cores of networks, we demonstrate that some of them are trivial and regular in ResNet.

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