A Physics-Informed Deep Learning Model for MRI Brain Motion Correction

Background: MRI is crucial for brain imaging but is highly susceptible to motion artifacts due to long acquisition times. This study introduces PI-MoCoNet, a physics-informed motion correction network that integrates spatial and k-space information to remove motion artifacts without explicit motion parameter estimation, enhancing image fidelity and diagnostic reliability. Materials and Methods: PI-MoCoNet consists of a motion detection network (U-net with spatial averaging) to identify corrupted k-space lines and a motion correction network (U-net with Swin Transformer blocks) to reconstruct motion-free images. The correction is guided by three loss functions: reconstruction (L1), perceptual (LPIPS), and data consistency (Ldc). Motion artifacts were simulated via rigid phase encoding perturbations and evaluated on IXI and MR-ART datasets against Pix2Pix, CycleGAN, and U-net using PSNR, SSIM, and NMSE. Results: PI-MoCoNet significantly improved image quality. On IXI, for minor artifacts, PSNR increased from 34.15 dB to 45.95 dB, SSIM from 0.87 to 1.00, and NMSE reduced from 0.55% to 0.04%. For moderate artifacts, PSNR improved from 30.23 dB to 42.16 dB, SSIM from 0.80 to 0.99, and NMSE from 1.32% to 0.09%. For heavy artifacts, PSNR rose from 27.99 dB to 36.01 dB, SSIM from 0.75 to 0.97, and NMSE decreased from 2.21% to 0.36%. On MR-ART, PI-MoCoNet achieved PSNR gains of ~10 dB and SSIM improvements of up to 0.20, with NMSE reductions of ~6%. Ablation studies confirmed the importance of data consistency and perceptual losses, yielding a 1 dB PSNR gain and 0.17% NMSE reduction. Conclusions: PI-MoCoNet effectively mitigates motion artifacts in brain MRI, outperforming existing methods. Its ability to integrate spatial and k-space information makes it a promising tool for clinical use in motion-prone settings. Code: https://github.com/mosaf/PI-MoCoNet.git.

Advancing MRI Reconstruction: A Systematic Review of Deep Learning and Compressed Sensing Integration

Magnetic resonance imaging (MRI) is a non-invasive imaging modality and provides comprehensive anatomical and functional insights into the human body. However, its long acquisition times can lead to patient discomfort, motion artifacts, and limiting real-time applications. To address these challenges, strategies such as parallel imaging have been applied, which utilize multiple receiver coils to speed up the data acquisition process. Additionally, compressed sensing (CS) is a method that facilitates image reconstruction from sparse data, significantly reducing image acquisition time by minimizing the amount of data collection needed. Recently, deep learning (DL) has emerged as a powerful tool for improving MRI reconstruction. It has been integrated with parallel imaging and CS principles to achieve faster and more accurate MRI reconstructions. This review comprehensively examines DL-based techniques for MRI reconstruction. We categorize and discuss various DL-based methods, including end-to-end approaches, unrolled optimization, and federated learning, highlighting their potential benefits. Our systematic review highlights significant contributions and underscores the potential of DL in MRI reconstruction. Additionally, we summarize key results and trends in DL-based MRI reconstruction, including quantitative metrics, the dataset, acceleration factors, and the progress of and research interest in DL techniques over time. Finally, we discuss potential future directions and the importance of DL-based MRI reconstruction in advancing medical imaging. To facilitate further research in this area, we provide a GitHub repository that includes up-to-date DL-based MRI reconstruction publications and public datasets-https://github.com/mosaf/Awesome-DL-based-CS-MRI.

Image-Domain Material Decomposition for Dual-energy CT using Unsupervised Learning with Data-fidelity Loss

Background: Dual-energy CT (DECT) and material decomposition play vital roles in quantitative medical imaging. However, the decomposition process may suffer from significant noise amplification, leading to severely degraded image signal-to-noise ratios (SNRs). While existing iterative algorithms perform noise suppression using different image priors, these heuristic image priors cannot accurately represent the features of the target image manifold. Although deep learning-based decomposition methods have been reported, these methods are in the supervised-learning framework requiring paired data for training, which is not readily available in clinical settings. Purpose: This work aims to develop an unsupervised-learning framework with data-measurement consistency for image-domain material decomposition in DECT.

Full-dose PET Synthesis from Low-dose PET Using High-efficiency Diffusion Denoising Probabilistic Model

To reduce the risks associated with ionizing radiation, a reduction of radiation exposure in PET imaging is needed. However, this leads to a detrimental effect on image contrast and quantification. High-quality PET images synthesized from low-dose data offer a solution to reduce radiation exposure. We introduce a diffusion-model-based approach for estimating full-dose PET images from low-dose ones: the PET Consistency Model (PET-CM) yielding synthetic quality comparable to state-of-the-art diffusion-based synthesis models, but with greater efficiency. There are two steps: a forward process that adds Gaussian noise to a full dose PET image at multiple timesteps, and a reverse diffusion process that employs a PET Shifted-window Vision Transformer (PET-VIT) network to learn the denoising procedure conditioned on the corresponding low-dose PETs. In PET-CM, the reverse process learns a consistency function for direct denoising of Gaussian noise to a clean full-dose PET. We evaluated the PET-CM in generating full-dose images using only 1/8 and 1/4 of the standard PET dose. Comparing 1/8 dose to full-dose images, PET-CM demonstrated impressive performance with normalized mean absolute error (NMAE) of 1.233+/-0.131%, peak signal-to-noise ratio (PSNR) of 33.915+/-0.933dB, structural similarity index (SSIM) of 0.964+/-0.009, and normalized cross-correlation (NCC) of 0.968+/-0.011, with an average generation time of 62 seconds per patient. This is a significant improvement compared to the state-of-the-art diffusion-based model with PET-CM reaching this result 12x faster. In the 1/4 dose to full-dose image experiments, PET-CM is also competitive, achieving an NMAE 1.058+/-0.092%, PSNR of 35.548+/-0.805dB, SSIM of 0.978+/-0.005, and NCC 0.981+/-0.007 The results indicate promising low-dose PET image quality improvements for clinical applications.

Synthetic CT Generation from MRI using 3D Transformer-based Denoising Diffusion Model

Magnetic resonance imaging (MRI)-based synthetic computed tomography (sCT) simplifies radiation therapy treatment planning by eliminating the need for CT simulation and error-prone image registration, ultimately reducing patient radiation dose and setup uncertainty. We propose an MRI-to-CT transformer-based denoising diffusion probabilistic model (MC-DDPM) to transform MRI into high-quality sCT to facilitate radiation treatment planning. MC-DDPM implements diffusion processes with a shifted-window transformer network to generate sCT from MRI. The proposed model consists of two processes: a forward process which adds Gaussian noise to real CT scans, and a reverse process in which a shifted-window transformer V-net (Swin-Vnet) denoises the noisy CT scans conditioned on the MRI from the same patient to produce noise-free CT scans. With an optimally trained Swin-Vnet, the reverse diffusion process was used to generate sCT scans matching MRI anatomy. We evaluated the proposed method by generating sCT from MRI on a brain dataset and a prostate dataset. Qualitative evaluation was performed using the mean absolute error (MAE) of Hounsfield unit (HU), peak signal to noise ratio (PSNR), multi-scale Structure Similarity index (MS-SSIM) and normalized cross correlation (NCC) indexes between ground truth CTs and sCTs. MC-DDPM generated brain sCTs with state-of-the-art quantitative results with MAE 43.317 HU, PSNR 27.046 dB, SSIM 0.965, and NCC 0.983. For the prostate dataset, MC-DDPM achieved MAE 59.953 HU, PSNR 26.920 dB, SSIM 0.849, and NCC 0.948. In conclusion, we have developed and validated a novel approach for generating CT images from routine MRIs using a transformer-based DDPM. This model effectively captures the complex relationship between CT and MRI images, allowing for robust and high-quality synthetic CT (sCT) images to be generated in minutes.

Cycle-guided Denoising Diffusion Probability Model for 3D Cross-modality MRI Synthesis

This study aims to develop a novel Cycle-guided Denoising Diffusion Probability Model (CG-DDPM) for cross-modality MRI synthesis. The CG-DDPM deploys two DDPMs that condition each other to generate synthetic images from two different MRI pulse sequences. The two DDPMs exchange random latent noise in the reverse processes, which helps to regularize both DDPMs and generate matching images in two modalities. This improves image-to-image translation ac-curacy. We evaluated the CG-DDPM quantitatively using mean absolute error (MAE), multi-scale structural similarity index measure (MSSIM), and peak sig-nal-to-noise ratio (PSNR), as well as the network synthesis consistency, on the BraTS2020 dataset. Our proposed method showed high accuracy and reliable consistency for MRI synthesis. In addition, we compared the CG-DDPM with several other state-of-the-art networks and demonstrated statistically significant improvements in the image quality of synthetic MRIs. The proposed method enhances the capability of current multimodal MRI synthesis approaches, which could contribute to more accurate diagnosis and better treatment planning for patients by synthesizing additional MRI modalities.

Cost-Sensitive Reference Pair Encoding for Multi-Label Learning

Label space expansion for multi-label classification (MLC) is a methodology that encodes the original label vectors to higher dimensional codes before training and decodes the predicted codes back to the label vectors during testing. The methodology has been demonstrated to improve the performance of MLC algorithms when coupled with off-the-shelf error-correcting codes for encoding and decoding. Nevertheless, such a coding scheme can be complicated to implement, and cannot easily satisfy a common application need of cost-sensitive MLC---adapting to different evaluation criteria of interest. In this work, we show that a simpler coding scheme based on the concept of a reference pair of label vectors achieves cost-sensitivity more naturally. In particular, our proposed cost-sensitive reference pair encoding (CSRPE) algorithm contains cluster-based encoding, weight-based training and voting-based decoding steps, all utilizing the cost information. Furthermore, we leverage the cost information embedded in the code space of CSRPE to propose a novel active learning algorithm for cost-sensitive MLC. Extensive experimental results verify that CSRPE performs better than state-of-the-art algorithms across different MLC criteria. The results also demonstrate that the CSRPE-backed active learning algorithm is superior to existing algorithms for active MLC, and further justify the usefulness of CSRPE.

RubyStar: A Non-Task-Oriented Mixture Model Dialog System

RubyStar is a dialog system designed to create "human-like" conversation by combining different response generation strategies. RubyStar conducts a non-task-oriented conversation on general topics by using an ensemble of rule-based, retrieval-based and generative methods. Topic detection, engagement monitoring, and context tracking are used for managing interaction. Predictable elements of conversation, such as the bot's backstory and simple question answering are handled by separate modules. We describe a rating scheme we developed for evaluating response generation. We find that character-level RNN is an effective generation model for general responses, with proper parameter settings; however other kinds of conversation topics might benefit from using other models.