Spatial-Angular Representation Learning for High-Fidelity Continuous Super-Resolution in Diffusion MRI

Diffusion magnetic resonance imaging (dMRI) often suffers from low spatial and angular resolution due to inherent limitations in imaging hardware and system noise, adversely affecting the accurate estimation of microstructural parameters with fine anatomical details. Deep learning-based super-resolution techniques have shown promise in enhancing dMRI resolution without increasing acquisition time. However, most existing methods are confined to either spatial or angular super-resolution, limiting their effectiveness in capturing detailed microstructural features. Furthermore, traditional pixel-wise loss functions struggle to recover intricate image details essential for high-resolution reconstruction. To address these challenges, we propose SARL-dMRI, a novel Spatial-Angular Representation Learning framework for high-fidelity, continuous super-resolution in dMRI. SARL-dMRI explores implicit neural representations and spherical harmonics to model continuous spatial and angular representations, simultaneously enhancing both spatial and angular resolution while improving microstructural parameter estimation accuracy. To further preserve image fidelity, a data-fidelity module and wavelet-based frequency loss are introduced, ensuring the super-resolved images remain consistent with the original input and retain fine details. Extensive experiments demonstrate that, compared to five other state-of-the-art methods, our method significantly enhances dMRI data resolution, improves the accuracy of microstructural parameter estimation, and provides better generalization capabilities. It maintains stable performance even under a 45$\times$ downsampling factor.

Leveraging Video Vision Transformer for Alzheimer's Disease Diagnosis from 3D Brain MRI

Alzheimer's disease (AD) is a neurodegenerative disorder affecting millions worldwide, necessitating early and accurate diagnosis for optimal patient management. In recent years, advancements in deep learning have shown remarkable potential in medical image analysis. Methods In this study, we present "ViTranZheimer," an AD diagnosis approach which leverages video vision transformers to analyze 3D brain MRI data. By treating the 3D MRI volumes as videos, we exploit the temporal dependencies between slices to capture intricate structural relationships. The video vision transformer's self-attention mechanisms enable the model to learn long-range dependencies and identify subtle patterns that may indicate AD progression. Our proposed deep learning framework seeks to enhance the accuracy and sensitivity of AD diagnosis, empowering clinicians with a tool for early detection and intervention. We validate the performance of the video vision transformer using the ADNI dataset and conduct comparative analyses with other relevant models. Results The proposed ViTranZheimer model is compared with two hybrid models, CNN-BiLSTM and ViT-BiLSTM. CNN-BiLSTM is the combination of a convolutional neural network (CNN) and a bidirectional long-short-term memory network (BiLSTM), while ViT-BiLSTM is the combination of a vision transformer (ViT) with BiLSTM. The accuracy levels achieved in the ViTranZheimer, CNN-BiLSTM, and ViT-BiLSTM models are 98.6%, 96.479%, and 97.465%, respectively. ViTranZheimer demonstrated the highest accuracy at 98.6%, outperforming other models in this evaluation metric, indicating its superior performance in this specific evaluation metric. Conclusion This research advances the understanding of applying deep learning techniques in neuroimaging and Alzheimer's disease research, paving the way for earlier and less invasive clinical diagnosis.

Pfungst and Clever Hans: Identifying the unintended cues in a widely used Alzheimer's disease MRI dataset using explainable deep learning

Backgrounds. Deep neural networks have demonstrated high accuracy in classifying Alzheimer's disease (AD). This study aims to enlighten the underlying black-box nature and reveal individual contributions of T1-weighted (T1w) gray-white matter texture, volumetric information and preprocessing on classification performance. Methods. We utilized T1w MRI data from the Alzheimer's Disease Neuroimaging Initiative to distinguish matched AD patients (990 MRIs) from healthy controls (990 MRIs). Preprocessing included skull stripping and binarization at varying thresholds to systematically eliminate texture information. A deep neural network was trained on these configurations, and the model performance was compared using McNemar tests with discrete Bonferroni-Holm correction. Layer-wise Relevance Propagation (LRP) and structural similarity metrics between heatmaps were applied to analyze learned features. Results. Classification performance metrics (accuracy, sensitivity, and specificity) were comparable across all configurations, indicating a negligible influence of T1w gray- and white signal texture. Models trained on binarized images demonstrated similar feature performance and relevance distributions, with volumetric features such as atrophy and skull-stripping features emerging as primary contributors. Conclusions. We revealed a previously undiscovered Clever Hans effect in a widely used AD MRI dataset. Deep neural networks classification predominantly rely on volumetric features, while eliminating gray-white matter T1w texture did not decrease the performance. This study clearly demonstrates an overestimation of the importance of gray-white matter contrasts, at least for widely used structural T1w images, and highlights potential misinterpretation of performance metrics.

Stroke Lesion Segmentation using Multi-Stage Cross-Scale Attention

Precise characterization of stroke lesions from MRI data has immense value in prognosticating clinical and cognitive outcomes following a stroke. Manual stroke lesion segmentation is time-consuming and requires the expertise of neurologists and neuroradiologists. Often, lesions are grossly characterized for their location and overall extent using bounding boxes without specific delineation of their boundaries. While such characterization provides some clinical value, to develop a precise mechanistic understanding of the impact of lesions on post-stroke vascular contributions to cognitive impairments and dementia (VCID), the stroke lesions need to be fully segmented with accurate boundaries. This work introduces the Multi-Stage Cross-Scale Attention (MSCSA) mechanism, applied to the U-Net family, to improve the mapping between brain structural features and lesions of varying sizes. Using the Anatomical Tracings of Lesions After Stroke (ATLAS) v2.0 dataset, MSCSA outperforms all baseline methods in both Dice and F1 scores on a subset focusing on small lesions, while maintaining competitive performance across the entire dataset. Notably, the ensemble strategy incorporating MSCSA achieves the highest scores for Dice and F1 on both the full dataset and the small lesion subset. These results demonstrate the effectiveness of MSCSA in segmenting small lesions and highlight its robustness across different training schemes for large stroke lesions. Our code is available at: https://github.com/nadluru/StrokeLesSeg.

Foundations of a Knee Joint Digital Twin from qMRI Biomarkers for Osteoarthritis and Knee Replacement

This study forms the basis of a digital twin system of the knee joint, using advanced quantitative MRI (qMRI) and machine learning to advance precision health in osteoarthritis (OA) management and knee replacement (KR) prediction. We combined deep learning-based segmentation of knee joint structures with dimensionality reduction to create an embedded feature space of imaging biomarkers. Through cross-sectional cohort analysis and statistical modeling, we identified specific biomarkers, including variations in cartilage thickness and medial meniscus shape, that are significantly associated with OA incidence and KR outcomes. Integrating these findings into a comprehensive framework represents a considerable step toward personalized knee-joint digital twins, which could enhance therapeutic strategies and inform clinical decision-making in rheumatological care. This versatile and reliable infrastructure has the potential to be extended to broader clinical applications in precision health.

AI-Driven Secure Data Sharing: A Trustworthy and Privacy-Preserving Approach

In the era of data-driven decision-making, ensuring the privacy and security of shared data is paramount across various domains. Applying existing deep neural networks (DNNs) to encrypted data is critical and often compromises performance, security, and computational overhead. To address these limitations, this research introduces a secure framework consisting of a learnable encryption method based on the block-pixel operation to encrypt the data and subsequently integrate it with the Vision Transformer (ViT). The proposed framework ensures data privacy and security by creating unique scrambling patterns per key, providing robust performance against adversarial attacks without compromising computational efficiency and data integrity. The framework was tested on sensitive medical datasets to validate its efficacy, proving its ability to handle highly confidential information securely. The suggested framework was validated with a 94\% success rate after extensive testing on real-world datasets, such as MRI brain tumors and histological scans of lung and colon cancers. Additionally, the framework was tested under diverse adversarial attempts against secure data sharing with optimum performance and demonstrated its effectiveness in various threat scenarios. These comprehensive analyses underscore its robustness, making it a trustworthy solution for secure data sharing in critical applications.

Investigating the Feasibility of Patch-based Inference for Generalized Diffusion Priors in Inverse Problems for Medical Images

Plug-and-play approaches to solving inverse problems such as restoration and super-resolution have recently benefited from Diffusion-based generative priors for natural as well as medical images. However, solutions often use the standard albeit computationally intensive route of training and inferring with the whole image on the diffusion prior. While patch-based approaches to evaluating diffusion priors in plug-and-play methods have received some interest, they remain an open area of study. In this work, we explore the feasibility of the usage of patches for training and inference of a diffusion prior on MRI images. We explore the minor adaptation necessary for artifact avoidance, the performance and the efficiency of memory usage of patch-based methods as well as the adaptability of whole image training to patch-based evaluation - evaluating across multiple plug-and-play methods, tasks and datasets.

Sparse Mixture-of-Experts for Non-Uniform Noise Reduction in MRI Images

Magnetic Resonance Imaging (MRI) is an essential diagnostic tool in clinical settings, but its utility is often hindered by noise artifacts introduced during the imaging process.Effective denoising is critical for enhancing image quality while preserving anatomical structures. However, traditional denoising methods, which often assume uniform noise distributions, struggle to handle the non-uniform noise commonly present in MRI images. In this paper, we introduce a novel approach leveraging a sparse mixture-of-experts framework for MRI image denoising. Each expert is a specialized denoising convolutional neural network fine-tuned to target specific noise characteristics associated with different image regions. Our method demonstrates superior performance over state-of-the-art denoising techniques on both synthetic and real-world brain MRI datasets. Furthermore, we show that it generalizes effectively to unseen datasets, highlighting its robustness and adaptability.

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.

Fully Guided Neural Schrödinger bridge for Brain MR image synthesis

Multi-modal brain MRI provides essential complementary information for clinical diagnosis. However, acquiring all modalities is often challenging due to time and cost constraints. To address this, various methods have been proposed to generate missing modalities from available ones. Traditional approaches can be broadly categorized into two main types: paired and unpaired methods. While paired methods offer superior performance, obtaining large-scale paired datasets is challenging in real-world scenarios. Conversely, unpaired methods facilitate large-scale data collection but struggle to preserve critical image features, such as tumors. In this paper, we propose Fully Guided Schr\"odinger Bridges (FGSB), a novel framework based on Neural Schr\"odinger Bridges, to overcome these limitations. FGSB achieves stable, high-quality generation of missing modalities using minimal paired data. Furthermore, when provided with ground truth or a segmentation network for specific regions, FGSB can generate missing modalities while preserving these critical areas with reduced data requirements. Our proposed model consists of two consecutive phases. 1) Generation Phase: Fuses a generated image, a paired reference image, and Gaussian noise, employing iterative refinement to mitigate issues such as mode collapse and improve generation quality 2) Training Phase: Learns the mapping from the generated image to the target modality. Experiments demonstrate that FGSB achieves comparable generation performance to methods trained on large datasets, while using data from only two subjects. Moreover, the utilization of lesion information with FGSB significantly enhances its ability to preserve crucial lesion features.