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.

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

Incoherent k-space under-sampling 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. Comprehensive experiments were conducted on both publicly available fastMRI images and an in-house multi-echo GRE (QSM) subject. Overall, the results showed that SSDM-MRI outperformed other methods in terms of numerical metrics (PSNR and SSIM), qualitative error maps, image fine details, and latent susceptibility information hidden in MRI phase images. In addition, the reconstruction time for a 320*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.

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.

Bi-level Guided Diffusion Models for Zero-Shot Medical Imaging Inverse Problems

In the realm of medical imaging, inverse problems aim to infer high-quality images from incomplete, noisy measurements, with the objective of minimizing expenses and risks to patients in clinical settings. The Diffusion Models have recently emerged as a promising approach to such practical challenges, proving particularly useful for the zero-shot inference of images from partially acquired measurements in Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). A central challenge in this approach, however, is how to guide an unconditional prediction to conform to the measurement information. Existing methods rely on deficient projection or inefficient posterior score approximation guidance, which often leads to suboptimal performance. In this paper, we propose \underline{\textbf{B}}i-level \underline{G}uided \underline{D}iffusion \underline{M}odels ({BGDM}), a zero-shot imaging framework that efficiently steers the initial unconditional prediction through a \emph{bi-level} guidance strategy. Specifically, BGDM first approximates an \emph{inner-level} conditional posterior mean as an initial measurement-consistent reference point and then solves an \emph{outer-level} proximal optimization objective to reinforce the measurement consistency. Our experimental findings, using publicly available MRI and CT medical datasets, reveal that BGDM is more effective and efficient compared to the baselines, faithfully generating high-fidelity medical images and substantially reducing hallucinatory artifacts in cases of severe degradation.

QSMDiff: Unsupervised 3D Diffusion Models for Quantitative Susceptibility Mapping

Quantitative Susceptibility Mapping (QSM) dipole inversion is an ill-posed inverse problem for quantifying magnetic susceptibility distributions from MRI tissue phases. While supervised deep learning methods have shown success in specific QSM tasks, their generalizability across different acquisition scenarios remains constrained. Recent developments in diffusion models have demonstrated potential for solving 2D medical imaging inverse problems. However, their application to 3D modalities, such as QSM, remains challenging due to high computational demands. In this work, we developed a 3D image patch-based diffusion model, namely QSMDiff, for robust QSM reconstruction across different scan parameters, alongside simultaneous super-resolution and image-denoising tasks. QSMDiff adopts unsupervised 3D image patch training and full-size measurement guidance during inference for controlled image generation. Evaluation on simulated and in-vivo human brains, using gradient-echo and echo-planar imaging sequences across different acquisition parameters, demonstrates superior performance. The method proposed in QSMDiff also holds promise for impacting other 3D medical imaging applications beyond QSM.

Fast Controllable Diffusion Models for Undersampled MRI Reconstruction

Supervised deep learning methods have shown promise in undersampled Magnetic Resonance Imaging (MRI) reconstruction, but their requirement for paired data limits their generalizability to the diverse MRI acquisition parameters. Recently, unsupervised controllable generative diffusion models have been applied to undersampled MRI reconstruction, without paired data or model retraining for different MRI acquisitions. However, diffusion models are generally slow in sampling and state-of-the-art acceleration techniques can lead to sub-optimal results when directly applied to the controllable generation process. This study introduces a new algorithm called Predictor-Projector-Noisor (PPN), which enhances and accelerates controllable generation of diffusion models for undersampled MRI reconstruction. Our results demonstrate that PPN produces high-fidelity MR images that conform to undersampled k-space measurements with significantly shorter reconstruction time than other controllable sampling methods. In addition, the unsupervised PPN accelerated diffusion models are adaptable to different MRI acquisition parameters, making them more practical for clinical use than supervised learning techniques.

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.

Multi-scale MRI reconstruction via dilated ensemble networks

As aliasing artefacts are highly structural and non-local, many MRI reconstruction networks use pooling to enlarge filter coverage and incorporate global context. However, this inadvertently impedes fine detail recovery as downsampling creates a resolution bottleneck. Moreover, real and imaginary features are commonly split into separate channels, discarding phase information particularly important to high frequency textures. In this work, we introduce an efficient multi-scale reconstruction network using dilated convolutions to preserve resolution and experiment with a complex-valued version using complex convolutions. Inspired by parallel dilated filters, multiple receptive fields are processed simultaneously with branches that see both large structural artefacts and fine local features. We also adopt dense residual connections for feature aggregation to efficiently increase scale and the deep cascade global architecture to reduce overfitting. The real-valued version of this model outperformed common reconstruction architectures as well as a state-of-the-art multi-scale network whilst being three times more efficient. The complex-valued network yielded better qualitative results when more phase information was present.

Quantitative Susceptibility Mapping through Model-based Deep Image Prior (MoDIP)

The data-driven approach of supervised learning methods has limited applicability in solving dipole inversion in Quantitative Susceptibility Mapping (QSM) with varying scan parameters across different objects. To address this generalization issue in supervised QSM methods, we propose a novel training-free model-based unsupervised method called MoDIP (Model-based Deep Image Prior). MoDIP comprises a small, untrained network and a Data Fidelity Optimization (DFO) module. The network converges to an interim state, acting as an implicit prior for image regularization, while the optimization process enforces the physical model of QSM dipole inversion. Experimental results demonstrate MoDIP's excellent generalizability in solving QSM dipole inversion across different scan parameters. It exhibits robustness against pathological brain QSM, achieving over 32% accuracy improvement than supervised deep learning and traditional iterative methods. It is also 33% more computationally efficient and runs 4 times faster than conventional DIP-based approaches, enabling 3D high-resolution image reconstruction in under 4.5 minutes.

MM-SFENet: Multi-scale Multi-task Localization and Classification of Bladder Cancer in MRI with Spatial Feature Encoder Network

Background and Objective: Bladder cancer is a common malignant urinary carcinoma, with muscle-invasive and non-muscle-invasive as its two major subtypes. This paper aims to achieve automated bladder cancer invasiveness localization and classification based on MRI. Method: Different from previous efforts that segment bladder wall and tumor, we propose a novel end-to-end multi-scale multi-task spatial feature encoder network (MM-SFENet) for locating and classifying bladder cancer, according to the classification criteria of the spatial relationship between the tumor and bladder wall. First, we built a backbone with residual blocks to distinguish bladder wall and tumor; then, a spatial feature encoder is designed to encode the multi-level features of the backbone to learn the criteria. Results: We substitute Smooth-L1 Loss with IoU Loss for multi-task learning, to improve the accuracy of the classification task. By testing a total of 1287 MRIs collected from 98 patients at the hospital, the mAP and IoU are used as the evaluation metrics. The experimental result could reach 93.34\% and 83.16\% on test set. Conclusions: The experimental result demonstrates the effectiveness of the proposed MM-SFENet on the localization and classification of bladder cancer. It may provide an effective supplementary diagnosis method for bladder cancer staging.