Quantification of brain atrophy currently requires visual rating scales which are time consuming and automated brain image analysis is warranted. We validated our automated deep learning (DL) tool measuring the Global Cerebral Atrophy (GCA) score against trained human raters, and associations with age and cognitive impairment, in representative older (>65 years) patients. CT-brain scans were obtained from patients in acute medicine (ORCHARD-EPR), acute stroke (OCS studies) and a legacy sample. Scans were divided in a 60/20/20 ratio for training, optimisation and testing. CT-images were assessed by two trained raters (rater-1=864 scans, rater-2=20 scans). Agreement between DL tool-predicted GCA scores (range 0-39) and the visual ratings was evaluated using mean absolute error (MAE) and Cohen's weighted kappa. Among 864 scans (ORCHARD-EPR=578, OCS=200, legacy scans=86), MAE between the DL tool and rater-1 GCA scores was 3.2 overall, 3.1 for ORCHARD-EPR, 3.3 for OCS and 2.6 for the legacy scans and half had DL-predicted GCA error between -2 and 2. Inter-rater agreement was Kappa=0.45 between the DL-tool and rater-1, and 0.41 between the tool and rater- 2 whereas it was lower at 0.28 for rater-1 and rater-2. There was no difference in GCA scores from the DL-tool and the two raters (one-way ANOVA, p=0.35) or in mean GCA scores between the DL-tool and rater-1 (paired t-test, t=-0.43, p=0.66), the tool and rater-2 (t=1.35, p=0.18) or between rater-1 and rater-2 (t=0.99, p=0.32). DL-tool GCA scores correlated with age and cognitive scores (both p<0.001). Our DL CT-brain analysis tool measured GCA score accurately and without user input in real-world scans acquired from older patients. Our tool will enable extraction of standardised quantitative measures of atrophy at scale for use in health data research and will act as proof-of-concept towards a point-of-care clinically approved tool.

Vision foundation models like DINOv2 demonstrate remarkable potential in medical imaging despite their origin in natural image domains. However, their design inherently works best for uni-modal image analysis, limiting their effectiveness for multi-modal imaging tasks that are common in many medical fields, such as neurology and oncology. While supervised models perform well in this setting, they fail to leverage unlabeled datasets and struggle with missing modalities, a frequent challenge in clinical settings. To bridge these gaps, we introduce MM-DINOv2, a novel and efficient framework that adapts the pre-trained vision foundation model DINOv2 for multi-modal medical imaging. Our approach incorporates multi-modal patch embeddings, enabling vision foundation models to effectively process multi-modal imaging data. To address missing modalities, we employ full-modality masking, which encourages the model to learn robust cross-modality relationships. Furthermore, we leverage semi-supervised learning to harness large unlabeled datasets, enhancing both the accuracy and reliability of medical predictions. Applied to glioma subtype classification from multi-sequence brain MRI, our method achieves a Matthews Correlation Coefficient (MCC) of 0.6 on an external test set, surpassing state-of-the-art supervised approaches by +11.1%. Our work establishes a scalable and robust solution for multi-modal medical imaging tasks, leveraging powerful vision foundation models pre-trained on natural images while addressing real-world clinical challenges such as missing data and limited annotations.

This retrospective-prospective study evaluated whether a deep learning-based MRI reconstruction algorithm can preserve diagnostic quality in brain MRI scans accelerated up to fourfold, using both public and prospective clinical data. The study included 18 healthy volunteers (scans acquired at 3T, January 2024-March 2025), as well as selected fastMRI public datasets with diverse pathologies. Phase-encoding-undersampled 2D/3D T1, T2, and FLAIR sequences were reconstructed with DeepFoqus-Accelerate and compared with standard-of-care (SOC). Three board-certified neuroradiologists and two MRI technologists independently reviewed 36 paired SOC/AI reconstructions from both datasets using a 5-point Likert scale, while quantitative similarity was assessed for 408 scans and 1224 datasets using Structural Similarity Index (SSIM), Peak Signal-to-Noise Ratio (PSNR), and Haar wavelet-based Perceptual Similarity Index (HaarPSI). No AI-reconstructed scan scored below 3 (minimally acceptable), and 95% scored $\geq 4$. Mean SSIM was 0.95 $\pm$ 0.03 (90% cases >0.90), PSNR >41.0 dB, and HaarPSI >0.94. Inter-rater agreement was slight to moderate. Rare artifacts did not affect diagnostic interpretation. These findings demonstrate that DeepFoqus-Accelerate enables robust fourfold brain MRI acceleration with 75% reduced scan time, while preserving diagnostic image quality and supporting improved workflow efficiency.

Accurate evaluation of the response of glioblastoma to therapy is crucial for clinical decision-making and patient management. The Response Assessment in Neuro-Oncology (RANO) criteria provide a standardized framework to assess patients' clinical response, but their application can be complex and subject to observer variability. This paper presents an automated method for classifying the intervention response from longitudinal MRI scans, developed to predict tumor response during therapy as part of the BraTS 2025 challenge. We propose a novel hybrid framework that combines deep learning derived feature extraction and an extensive set of radiomics and clinically chosen features. Our approach utilizes a fine-tuned ResNet-18 model to extract features from 2D regions of interest across four MRI modalities. These deep features are then fused with a rich set of more than 4800 radiomic and clinically driven features, including 3D radiomics of tumor growth and shrinkage masks, volumetric changes relative to the nadir, and tumor centroid shift. Using the fused feature set, a CatBoost classifier achieves a mean ROC AUC of 0.81 and a Macro F1 score of 0.50 in the 4-class response prediction task (Complete Response, Partial Response, Stable Disease, Progressive Disease). Our results highlight that synergizing learned image representations with domain-targeted radiomic features provides a robust and effective solution for automated treatment response assessment in neuro-oncology.

Brain tumors are serious health problems that require early diagnosis due to their high mortality rates. Diagnosing tumors by examining Magnetic Resonance Imaging (MRI) images is a process that requires expertise and is prone to error. Therefore, the need for automated diagnosis systems is increasing day by day. In this context, a robust and explainable Deep Learning (DL) model for the classification of brain tumors is proposed. In this study, a publicly available Figshare dataset containing 3,064 T1-weighted contrast-enhanced brain MRI images of three tumor types was used. First, the classification performance of nine well-known CNN architectures was evaluated to determine the most effective backbone. Among these, EfficientNetV2 demonstrated the best performance and was selected as the backbone for further development. Subsequently, an attention-based MLP-Mixer architecture was integrated into EfficientNetV2 to enhance its classification capability. The performance of the final model was comprehensively compared with basic CNNs and the methods in the literature. Additionally, Grad-CAM visualization was used to interpret and validate the decision-making process of the proposed model. The proposed model's performance was evaluated using the five-fold cross-validation method. The proposed model demonstrated superior performance with 99.50% accuracy, 99.47% precision, 99.52% recall and 99.49% F1 score. The results obtained show that the model outperforms the studies in the literature. Moreover, Grad-CAM visualizations demonstrate that the model effectively focuses on relevant regions of MRI images, thus improving interpretability and clinical reliability. A robust deep learning model for clinical decision support systems has been obtained by combining EfficientNetV2 and attention-based MLP-Mixer, providing high accuracy and interpretability in brain tumor classification.

Brain Metastases (BM) are a large contributor to mortality of patients with cancer. They are treated with Stereotactic Radiosurgery (SRS) and monitored with Magnetic Resonance Imaging (MRI) at regular follow-up intervals according to treatment guidelines. Analyzing and quantifying this longitudinal imaging represents an intractable workload for clinicians. As a result, follow-up images are not annotated and merely assessed by observation. Response to treatment in longitudinal imaging is being studied, to better understand growth trajectories and ultimately predict treatment success or toxicity as early as possible. In this study, we implement an automated pipeline to curate a large longitudinal dataset of SRS treatment data, resulting in a cohort of 896 BMs in 177 patients who were monitored for >360 days at approximately two-month intervals at Lausanne University Hospital (CHUV). We use a data-driven clustering to identify characteristic trajectories. In addition, we predict 12 months lesion-level response using classical as well as graph machine learning Graph Machine Learning (GML). Clustering revealed 5 dominant growth trajectories with distinct final response categories. Response prediction reaches up to 0.90 AUC (CI95%=0.88-0.92) using only pre-treatment and first follow-up MRI with gradient boosting. Similarly, robust predictive performance of up to 0.88 AUC (CI95%=0.86-0.90) was obtained using GML, offering more flexibility with a single model for multiple input time-points configurations. Our results suggest potential automation and increased precision for the comprehensive assessment and prediction of BM response to SRS in longitudinal MRI. The proposed pipeline facilitates scalable data curation for the investigation of BM growth patterns, and lays the foundation for clinical decision support systems aiming at optimizing personalized care.

We propose a Biophysically Restrained Analog Integrated Neural Network (BRAINN), an analog electrical network that models the dynamics of brain function. The network interconnects analog electrical circuits that simulate two tightly coupled brain processes: (1) propagation of an action potential, and (2) regional cerebral blood flow in response to the metabolic demands of signal propagation. These two processes are modeled by two branches of an electrical circuit comprising a resistor, a capacitor, and an inductor. We estimated the electrical components from in vivo multimodal MRI together with the biophysical properties of the brain applied to state-space equations, reducing arbitrary parameters such that the dynamic behavior is determined by neuronal integrity. Electrical circuits were interconnected at Brodmann areas to form a network using neural pathways traced with diffusion tensor imaging data. We built BRAINN in Simulink, MATLAB, using longitudinal multimodal MRI data from 20 healthy controls and 19 children with leukemia. BRAINN stimulated by an impulse applied to the lateral temporal region generated sustained activity. Stimulated BRAINN functional connectivity was comparable (within ±1.3 standard deviations) to measured resting-state functional connectivity in 40 of the 55 pairs of brain regions. Control system analyses showed that BRAINN was stable for all participants. BRAINN controllability in patients relative to healthy participants was disrupted prior to treatment but improved during treatment. BRAINN is scalable as more detailed regions and fiber tracts are traced in the MRI data. A scalable BRAINN will facilitate study of brain behavior in health and illness, and help identify targets and design transcranial stimulation for optimally modulating brain activity.

Diffusion MRI (dMRI) angular super-resolution (ASR) aims to reconstruct high-angular-resolution (HAR) signals from limited low-angular-resolution (LAR) data without prolonging scan time. However, existing methods are limited in recovering fine-grained angular details or preserving high fidelity due to inadequate modeling of q-space geometry and insufficient incorporation of physical constraints. In this paper, we introduce a Physics-Guided Diffusion Transformer (PGDiT) designed to explore physical priors throughout both training and inference stages. During training, a Q-space Geometry-Aware Module (QGAM) with b-vector modulation and random angular masking facilitates direction-aware representation learning, enabling the network to generate directionally consistent reconstructions with fine angular details from sparse and noisy data. In inference, a two-stage Spherical Harmonics-Guided Posterior Sampling (SHPS) enforces alignment with the acquired data, followed by heat-diffusion-based SH regularization to ensure physically plausible reconstructions. This coarse-to-fine refinement strategy mitigates oversmoothing and artifacts commonly observed in purely data-driven or generative models. Extensive experiments on general ASR tasks and two downstream applications, Diffusion Tensor Imaging (DTI) and Neurite Orientation Dispersion and Density Imaging (NODDI), demonstrate that PGDiT outperforms existing deep learning models in detail recovery and data fidelity. Our approach presents a novel generative ASR framework that offers high-fidelity HAR dMRI reconstructions, with potential applications in neuroscience and clinical research.

Vision-language models have demonstrated impressive capabilities in generating 2D images under various conditions; however the impressive performance of these models in 2D is largely enabled by extensive, readily available pretrained foundation models. Critically, comparable pretrained foundation models do not exist for 3D, significantly limiting progress in this domain. As a result, the potential of vision-language models to produce high-resolution 3D counterfactual medical images conditioned solely on natural language descriptions remains completely unexplored. Addressing this gap would enable powerful clinical and research applications, such as personalized counterfactual explanations, simulation of disease progression scenarios, and enhanced medical training by visualizing hypothetical medical conditions in realistic detail. Our work takes a meaningful step toward addressing this challenge by introducing a framework capable of generating high-resolution 3D counterfactual medical images of synthesized patients guided by free-form language prompts. We adapt state-of-the-art 3D diffusion models with enhancements from Simple Diffusion and incorporate augmented conditioning to improve text alignment and image quality. To our knowledge, this represents the first demonstration of a language-guided native-3D diffusion model applied specifically to neurological imaging data, where faithful three-dimensional modeling is essential to represent the brain's three-dimensional structure. Through results on two distinct neurological MRI datasets, our framework successfully simulates varying counterfactual lesion loads in Multiple Sclerosis (MS), and cognitive states in Alzheimer's disease, generating high-quality images while preserving subject fidelity in synthetically generated medical images. Our results lay the groundwork for prompt-driven disease progression analysis within 3D medical imaging.

Artificial intelligence (AI)-powered deep learning has advanced brain tumor diagnosis in Internet of Things (IoT)-healthcare systems, achieving high accuracy with large datasets. Brain health is critical to human life, and accurate diagnosis is essential for effective treatment. Magnetic Resonance Imaging (MRI) provides key data for brain tumor detection, serving as a major source of big data for AI-driven image classification. In this study, we classified glioma, meningioma, and pituitary tumors from MRI images using Region-based Convolutional Neural Network (R-CNN) and UNet architectures. We also applied Convolutional Neural Networks (CNN) and CNN-based transfer learning models such as Inception-V3, EfficientNetB4, and VGG19. Model performance was assessed using F-score, recall, precision, and accuracy. The Fast R-CNN achieved the best results with 99% accuracy, 98.5% F-score, 99.5% Area Under the Curve (AUC), 99.4% recall, and 98.5% precision. Combining R-CNN, UNet, and transfer learning enables earlier diagnosis and more effective treatment in IoT-healthcare systems, improving patient outcomes. IoT devices such as wearable monitors and smart imaging systems continuously collect real-time data, which AI algorithms analyze to provide immediate insights for timely interventions and personalized care. For external cohort cross-dataset validation, EfficientNetB2 achieved the strongest performance among fine-tuned EfficientNet models, with 92.11% precision, 92.11% recall/sensitivity, 95.96% specificity, 92.02% F1-score, and 92.23% accuracy. These findings underscore the robustness and reliability of AI models in handling diverse datasets, reinforcing their potential to enhance brain tumor classification and patient care in IoT healthcare environments.