Brain tumors are a significant challenge to human health as they impair the proper functioning of the brain and the general quality of life, thus requiring clinical intervention through early and accurate diagnosis. Although current state-of-the-art deep learning methods have achieved remarkable progress, there is still a gap in the representation learning of tumor-specific spatial characteristics and the robustness of the classification model on heterogeneous data. In this paper, we introduce a novel Pyramidal Attention-Based bi-partitioned T Network (PABT-Net) that combines the hierarchical pyramidal attention mechanism and T-block based bi-partitioned feature extraction, and a self-convolutional dilated neural classifier as the final task. Such an architecture increases the discriminability of the space and decreases the false forecasting by adaptively focusing on informative areas in brain MRI images. The model was thoroughly tested on three benchmark datasets, Figshare Brain Tumor Dataset, Sartaj Brain MRI Dataset, and Br35H Brain Tumor Dataset, containing 7023 images labeled in four tumor classes: glioma, meningioma, no tumor, and pituitary tumor. It attained an overall classification accuracy of 99.12%, a mean cross-validation accuracy of 98.77%, a Jaccard similarity index of 0.986, and a Cohen's Kappa value of 0.987, indicating superb generalization and clinical stability. The model's effectiveness is also confirmed by tumor-wise classification accuracies: 96.75%, 98.46%, and 99.57% in glioma, meningioma, and pituitary tumors, respectively. Comparative experiments with the state-of-the-art models, including VGG19, MobileNet, and NASNet, were carried out, and ablation studies proved the effectiveness of NASNet incorporation. To capture more prominent spatial-temporal patterns, we investigated hybrid networks, including NASNet with ANN, CNN, LSTM, and CNN-LSTM variants. The framework implements a strict nine-fold cross-validation procedure. It integrates a broad range of measures in its evaluation, including precision, recall, specificity, F1-score, AUC, confusion matrices, and the ROC analysis, consistent across distributions. In general, the PABT-Net model has high potential to be a clinically deployable, interpretable, state-of-the-art automated brain tumor classification model.

Cognitive behavioral therapy (CBT) and pharmacotherapy are primary treatments for major depressive disorder (MDD). However, their differential effects on the neural networks associated with rumination, or repetitive negative thinking, remain poorly understood. This study included 135 participants, whose rumination severity was measured using the rumination response scale (RRS) and whose resting brain activity was measured using functional magnetic resonance imaging (fMRI) at baseline and after 16 weeks. MDD patients received either standard CBT based on Beck's manual (n = 28) or pharmacotherapy (n = 32). Using a hidden Markov model, we observed that MDD patients exhibited increased activity in the default mode network (DMN) and decreased occupancies in the sensorimotor and central executive networks (CEN). The DMN occurrence rate correlated positively with rumination severity. CBT, while not specifically designed to target rumination, reduced DMN occurrence rate and facilitated transitions toward a CEN-dominant brain state as part of broader therapeutic effects. Pharmacotherapy shifted DMN activity to the posterior region of the brain. These findings suggest that CBT and pharmacotherapy modulate brain network dynamics related to rumination through distinct therapeutic pathways.

Image registration is a fundamental technique in the analysis of longitudinal and multi-phase CT images within clinical practice. However, most existing methods are tailored for single-organ applications, limiting their generalizability to other anatomical regions. This work presents TotalRegistrator, an image registration framework capable of aligning multiple anatomical regions simultaneously using a standard UNet architecture and a novel field decomposition strategy. The model is lightweight, requiring only 11GB of GPU memory for training. To train and evaluate our method, we constructed a large-scale longitudinal dataset comprising 695 whole-body (thorax-abdomen-pelvic) paired CT scans from individual patients acquired at different time points. We benchmarked TotalRegistrator against a generic classical iterative algorithm and a recent foundation model for image registration. To further assess robustness and generalizability, we evaluated our model on three external datasets: the public thoracic and abdominal datasets from the Learn2Reg challenge, and a private multiphase abdominal dataset from a collaborating hospital. Experimental results on the in-house dataset show that the proposed approach generally surpasses baseline methods in multi-organ abdominal registration, with a slight drop in lung alignment performance. On out-of-distribution datasets, it achieved competitive results compared to leading single-organ models, despite not being fine-tuned for those tasks, demonstrating strong generalizability. The source code will be publicly available at: https://github.com/DIAGNijmegen/oncology_image_registration.git.

Accurate estimation of intravoxel incoherent motion (IVIM) parameters from diffusion-weighted MRI remains challenging due to the ill-posed nature of the inverse problem and high sensitivity to noise, particularly in the perfusion compartment. In this work, we propose a probabilistic deep learning framework based on Deep Ensembles (DE) of Mixture Density Networks (MDNs), enabling estimation of total predictive uncertainty and decomposition into aleatoric (AU) and epistemic (EU) components. The method was benchmarked against non probabilistic neural networks, a Bayesian fitting approach and a probabilistic network with single Gaussian parametrization. Supervised training was performed on synthetic data, and evaluation was conducted on both simulated and two in vivo datasets. The reliability of the quantified uncertainties was assessed using calibration curves, output distribution sharpness, and the Continuous Ranked Probability Score (CRPS). MDNs produced more calibrated and sharper predictive distributions for the D and f parameters, although slight overconfidence was observed in D*. The Robust Coefficient of Variation (RCV) indicated smoother in vivo estimates for D* with MDNs compared to Gaussian model. Despite the training data covering the expected physiological range, elevated EU in vivo suggests a mismatch with real acquisition conditions, highlighting the importance of incorporating EU, which was allowed by DE. Overall, we present a comprehensive framework for IVIM fitting with uncertainty quantification, which enables the identification and interpretation of unreliable estimates. The proposed approach can also be adopted for fitting other physical models through appropriate architectural and simulation adjustments.

Magnetic Resonance Imaging (MRI) of the fetal brain has become a key tool for studying brain development in vivo. Yet, its assessment remains challenging due to variability in brain maturation, imaging protocols, and uncertain estimates of Gestational Age (GA). To overcome these, brain atlases provide a standardized reference framework that facilitates objective evaluation and comparison across subjects by aligning the atlas and subjects in a common coordinate system. In this work, we introduce a novel deep-learning framework for generating continuous, age-specific fetal brain atlases for real-time fetal brain tissue segmentation. The framework combines a direct registration model with a conditional discriminator. Trained on a curated dataset of 219 neurotypical fetal MRIs spanning from 21 to 37 weeks of gestation. The method achieves high registration accuracy, captures dynamic anatomical changes with sharp structural detail, and robust segmentation performance with an average Dice Similarity Coefficient (DSC) of 86.3% across six brain tissues. Furthermore, volumetric analysis of the generated atlases reveals detailed neurotypical growth trajectories, providing valuable insights into the maturation of the fetal brain. This approach enables individualized developmental assessment with minimal pre-processing and real-time performance, supporting both research and clinical applications. The model code is available at https://github.com/cirmuw/fetal-brain-atlas

Reliable uncertainty quantification is crucial for trustworthy decision-making and the deployment of AI models in medical imaging. While prior work has explored the ability of neural networks to quantify predictive, epistemic, and aleatoric uncertainties using an information-theoretical approach in synthetic or well defined data settings like natural image classification, its applicability to real life medical diagnosis tasks remains underexplored. In this study, we provide an extensive uncertainty quantification benchmark for multi-label chest X-ray classification using the MIMIC-CXR-JPG dataset. We evaluate 13 uncertainty quantification methods for convolutional (ResNet) and transformer-based (Vision Transformer) architectures across a wide range of tasks. Additionally, we extend Evidential Deep Learning, HetClass NNs, and Deep Deterministic Uncertainty to the multi-label setting. Our analysis provides insights into uncertainty estimation effectiveness and the ability to disentangle epistemic and aleatoric uncertainties, revealing method- and architecture-specific strengths and limitations.

Angle estimation is an important step in the Doppler ultrasound clinical workflow to measure blood velocity. It is widely recognized that incorrect angle estimation is a leading cause of error in Doppler-based blood velocity measurements. In this paper, we propose a deep learning-based approach for automated Doppler angle estimation. The approach was developed using 2100 human carotid ultrasound images including image augmentation. Five pre-trained models were used to extract images features, and these features were passed to a custom shallow network for Doppler angle estimation. Independently, measurements were obtained by a human observer reviewing the images for comparison. The mean absolute error (MAE) between the automated and manual angle estimates ranged from 3.9{\deg} to 9.4{\deg} for the models evaluated. Furthermore, the MAE for the best performing model was less than the acceptable clinical Doppler angle error threshold thus avoiding misclassification of normal velocity values as a stenosis. The results demonstrate potential for applying a deep-learning based technique for automated ultrasound Doppler angle estimation. Such a technique could potentially be implemented within the imaging software on commercial ultrasound scanners.

The diagnosis of medical diseases faces challenges such as the misdiagnosis of small lesions. Deep learning, particularly multimodal approaches, has shown great potential in the field of medical disease diagnosis. However, the differences in dimensionality between medical imaging and electronic health record data present challenges for effective alignment and fusion. To address these issues, we propose the Multimodal Multiscale Cross-Attention Fusion Network (MMCAF-Net). This model employs a feature pyramid structure combined with an efficient 3D multi-scale convolutional attention module to extract lesion-specific features from 3D medical images. To further enhance multimodal data integration, MMCAF-Net incorporates a multi-scale cross-attention module, which resolves dimensional inconsistencies, enabling more effective feature fusion. We evaluated MMCAF-Net on the Lung-PET-CT-Dx dataset, and the results showed a significant improvement in diagnostic accuracy, surpassing current state-of-the-art methods. The code is available at https://github.com/yjx1234/MMCAF-Net

Interpolating missing data in k-space is essential for accelerating imaging. However, existing methods, including convolutional neural network-based deep learning, primarily exploit local predictability while overlooking the inherent global dependencies in k-space. Recently, Transformers have demonstrated remarkable success in natural language processing and image analysis due to their ability to capture long-range dependencies. This inspires the use of Transformers for k-space interpolation to better exploit its global structure. However, their lack of interpretability raises concerns regarding the reliability of interpolated data. To address this limitation, we propose GPI-WT, a white-box Transformer framework based on Globally Predictable Interpolation (GPI) for k-space. Specifically, we formulate GPI from the perspective of annihilation as a novel k-space structured low-rank (SLR) model. The global annihilation filters in the SLR model are treated as learnable parameters, and the subgradients of the SLR model naturally induce a learnable attention mechanism. By unfolding the subgradient-based optimization algorithm of SLR into a cascaded network, we construct the first white-box Transformer specifically designed for accelerated MRI. Experimental results demonstrate that the proposed method significantly outperforms state-of-the-art approaches in k-space interpolation accuracy while providing superior interpretability.

Automated segmentation of multiple sclerosis (MS) lesions using multicontrast magnetic resonance (MR) images improves efficiency and reproducibility compared to manual delineation, with deep learning (DL) methods achieving state-of-the-art performance. However, these DL-based methods have yet to simultaneously optimize in-domain accuracy and out-of-domain generalization when trained on a single source with limited data, or their performance has been unsatisfactory. To fill this gap, we propose a method called UNISELF, which achieves high accuracy within a single training domain while demonstrating strong generalizability across multiple out-of-domain test datasets. UNISELF employs a novel test-time self-ensembled lesion fusion to improve segmentation accuracy, and leverages test-time instance normalization (TTIN) of latent features to address domain shifts and missing input contrasts. Trained on the ISBI 2015 longitudinal MS segmentation challenge training dataset, UNISELF ranks among the best-performing methods on the challenge test dataset. Additionally, UNISELF outperforms all benchmark methods trained on the same ISBI training data across diverse out-of-domain test datasets with domain shifts and missing contrasts, including the public MICCAI 2016 and UMCL datasets, as well as a private multisite dataset. These test datasets exhibit domain shifts and/or missing contrasts caused by variations in acquisition protocols, scanner types, and imaging artifacts arising from imperfect acquisition. Our code is available at https://github.com/uponacceptance.