As an important branch of machine learning pipelines in medical imaging, radiomics faces two major challenges namely reproducibility and accessibility. In this work, we introduce open-radiomics, a set of radiomics datasets along with a comprehensive radiomics pipeline based on our proposed technical protocol to investigate the effects of radiomics feature extraction on the reproducibility of the results. We curated large-scale radiomics datasets based on three open-source datasets; BraTS 2020 for high-grade glioma (HGG) versus low-grade glioma (LGG) classification and survival analysis, BraTS 2023 for O6-methylguanine-DNA methyltransferase (MGMT) classification, and non-small cell lung cancer (NSCLC) survival analysis from the Cancer Imaging Archive (TCIA). We used the BraTS 2020 open-source Magnetic Resonance Imaging (MRI) dataset to demonstrate how our proposed technical protocol could be utilized in radiomics-based studies. The cohort includes 369 adult patients with brain tumors (76 LGG, and 293 HGG). Using PyRadiomics library for LGG vs. HGG classification, we created 288 radiomics datasets; the combinations of 4 MRI sequences, 3 binWidths, 6 image normalization methods, and 4 tumor subregions. We used Random Forest classifiers, and for each radiomics dataset, we repeated the training-validation-test (60%/20%/20%) experiment with different data splits and model random states 100 times (28,800 test results) and calculated the Area Under the Receiver Operating Characteristic Curve (AUROC). Unlike binWidth and image normalization, the tumor subregion and imaging sequence significantly affected performance of the models. T1 contrast-enhanced sequence and the union of Necrotic and the non-enhancing tumor core subregions resulted in the highest AUROCs (average test AUROC 0.951, 95% confidence interval of (0.949, 0.952)). Although several settings and data splits (28 out of 28800) yielded test AUROC of 1, they were irreproducible. Our experiments demonstrate the sources of variability in radiomics pipelines (e.g., tumor subregion) can have a significant impact on the results, which may lead to superficial perfect performances that are irreproducible. Not applicable.

Lacunes, which are small fluid-filled cavities in the brain, are signs of cerebral small vessel disease and have been clinically associated with various neurodegenerative and cerebrovascular diseases. Hence, accurate detection of lacunes is crucial and is one of the initial steps for the precise diagnosis of these diseases. However, developing a robust and consistently reliable method for detecting lacunes is challenging because of the heterogeneity in their appearance, contrast, shape, and size. In this study, we propose a lacune detection method using the Segment Anything Model (SAM), guided by point prompts from a candidate prompt generator. The prompt generator initially detects potential lacunes with a high sensitivity using a composite loss function. The true lacunes are then selected using SAM by discriminating their characteristics from mimics such as the sulcus and enlarged perivascular spaces, imitating the clinicians' strategy of examining the potential lacunes along all three axes. False positives are further reduced by adaptive thresholds based on the region wise prevalence of lacunes. We evaluated our method on two diverse, multi-centric MRI datasets, VALDO and ISLES, comprising only FLAIR sequences. Despite diverse imaging conditions and significant variations in slice thickness (0.5-6 mm), our method achieved sensitivities of 84% and 92%, with average false positive rates of 0.05 and 0.06 per slice in ISLES and VALDO datasets respectively. The proposed method demonstrates robust performance across varied imaging conditions and outperformed the state-of-the-art methods, demonstrating its effectiveness in lacune detection and quantification.

Glioblastoma is one of the most aggressive and common brain tumors, with a median survival of 10-15 months. Predicting Overall Survival (OS) is critical for personalizing treatment strategies and aligning clinical decisions with patient outcomes. In this study, we propose a novel Artificial Intelligence (AI) approach for OS prediction using Magnetic Resonance Imaging (MRI) images, exploiting Vision Transformers (ViTs) to extract hidden features directly from MRI images, eliminating the need of tumor segmentation. Unlike traditional approaches, our method simplifies the workflow and reduces computational resource requirements. The proposed model was evaluated on the BRATS dataset, reaching an accuracy of 62.5% on the test set, comparable to the top-performing methods. Additionally, it demonstrated balanced performance across precision, recall, and F1 score, overcoming the best model in these metrics. The dataset size limits the generalization of the ViT which typically requires larger datasets compared to convolutional neural networks. This limitation in generalization is observed across all the cited studies. This work highlights the applicability of ViTs for downsampled medical imaging tasks and establishes a foundation for OS prediction models that are computationally efficient and do not rely on segmentation.

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

Alzheimer's disease (AD) progression follows a complex continuum from normal cognition (NC) through mild cognitive impairment (MCI) to dementia, yet most deep learning approaches oversimplify this into discrete classification tasks. This study introduces M$^3$AD, a novel multi-task multi-gate mixture of experts framework that jointly addresses diagnostic classification and cognitive transition modeling using structural MRI. We incorporate three key innovations: (1) an open-source T1-weighted sMRI preprocessing pipeline, (2) a unified learning framework capturing NC-MCI-AD transition patterns with demographic priors (age, gender, brain volume) for improved generalization, and (3) a customized multi-gate mixture of experts architecture enabling effective multi-task learning with structural MRI alone. The framework employs specialized expert networks for diagnosis-specific pathological patterns while shared experts model common structural features across the cognitive continuum. A two-stage training protocol combines SimMIM pretraining with multi-task fine-tuning for joint optimization. Comprehensive evaluation across six datasets comprising 12,037 T1-weighted sMRI scans demonstrates superior performance: 95.13% accuracy for three-class NC-MCI-AD classification and 99.15% for binary NC-AD classification, representing improvements of 4.69% and 0.55% over state-of-the-art approaches. The multi-task formulation simultaneously achieves 97.76% accuracy in predicting cognitive transition. Our framework outperforms existing methods using fewer modalities and offers a clinically practical solution for early intervention. Code: https://github.com/csyfjiang/M3AD.

Intracerebral hemorrhage (ICH) is a medical emergency that demands rapid and accurate diagnosis for optimal patient management. Hemorrhagic lesions' segmentation on CT scans is a necessary first step for acquiring quantitative imaging data that are becoming increasingly useful in the clinical setting. However, traditional manual segmentation is time-consuming and prone to inter-rater variability, creating a need for automated solutions. This study introduces a novel approach combining advanced deep learning models to segment extensive and morphologically variable ICH lesions in non-contrast CT scans. We propose a two-step methodology that begins with a user-defined loose bounding box around the lesion, followed by a fine-tuned YOLOv8-S object detection model to generate precise, slice-specific bounding boxes. These bounding boxes are then used to prompt the Medical Segment Anything Model for accurate lesion segmentation. Our pipeline achieves high segmentation accuracy with minimal supervision, demonstrating strong potential as a practical alternative to task-specific models. We evaluated the model on a dataset of 252 CT scans demonstrating high performance in segmentation accuracy and robustness. Finally, the resulting segmentation tool is integrated into a user-friendly web application prototype, offering clinicians a simple interface for lesion identification and radiomic quantification.

Accurate and efficient brain tumor segmentation remains a critical challenge in neuroimaging due to the heterogeneous nature of tumor subregions and the high computational cost of volumetric inference. In this paper, we propose EfficientGFormer, a novel architecture that integrates pretrained foundation models with graph-based reasoning and lightweight efficiency mechanisms for robust 3D brain tumor segmentation. Our framework leverages nnFormer as a modality-aware encoder, transforming multi-modal MRI volumes into patch-level embeddings. These features are structured into a dual-edge graph that captures both spatial adjacency and semantic similarity. A pruned, edge-type-aware Graph Attention Network (GAT) enables efficient relational reasoning across tumor subregions, while a distillation module transfers knowledge from a full-capacity teacher to a compact student model for real-time deployment. Experiments on the MSD Task01 and BraTS 2021 datasets demonstrate that EfficientGFormer achieves state-of-the-art accuracy with significantly reduced memory and inference time, outperforming recent transformer-based and graph-based baselines. This work offers a clinically viable solution for fast and accurate volumetric tumor delineation, combining scalability, interpretability, and generalization.

Accurate and early diagnosis of Alzheimer's Disease (AD) is crucial for timely interventions and treatment advancement. Functional Magnetic Resonance Imaging (fMRI), measuring brain blood-oxygen level changes over time, is a powerful AD-diagnosis tool. However, current fMRI-based AD diagnosis methods rely on noise-susceptible time-domain features and focus only on synchronous brain-region interactions in the same time phase, neglecting asynchronous ones. To overcome these issues, we propose Frequency-Time Fusion Graph Neural Network (FTF-GNN). It integrates frequency- and time-domain features for robust AD classification, considering both asynchronous and synchronous brain-region interactions. First, we construct a fully connected hypervariate graph, where nodes represent brain regions and their Blood Oxygen Level-Dependent (BOLD) values at a time series point. A Discrete Fourier Transform (DFT) transforms these BOLD values from the spatial to the frequency domain for frequency-component analysis. Second, a Fourier-based Graph Neural Network (FourierGNN) processes the frequency features to capture asynchronous brain region connectivity patterns. Third, these features are converted back to the time domain and reshaped into a matrix where rows represent brain regions and columns represent their frequency-domain features at each time point. Each brain region then fuses its frequency-domain features with position encoding along the time series, preserving temporal and spatial information. Next, we build a brain-region network based on synchronous BOLD value associations and input the brain-region network and the fused features into a Graph Convolutional Network (GCN) to capture synchronous brain region connectivity patterns. Finally, a fully connected network classifies the brain-region features. Experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate the method's effectiveness: Our model achieves 91.26% accuracy and 96.79% AUC in AD versus Normal Control (NC) classification, showing promising performance. For early-stage detection, it attains state-of-the-art performance in distinguishing NC from Late Mild Cognitive Impairment (LMCI) with 87.16% accuracy and 93.22% AUC. Notably, in the challenging task of differentiating LMCI from AD, FTF-GNN achieves optimal performance (85.30% accuracy, 94.56% AUC), while also delivering competitive results (77.40% accuracy, 91.17% AUC) in distinguishing Early MCI (EMCI) from LMCI-the most clinically complex subtype classification. These results indicate that leveraging complementary frequency- and time-domain information, along with considering asynchronous and synchronous brain-region interactions, can address existing approach limitations, offering a robust neuroimaging-based diagnostic solution.

The use of Convolutional Neural Networks (CNNs) has greatly improved the interpretation of medical images. However, conventional CNNs typically demand extensive computational resources and large training datasets. To address these limitations, this study applied transfer learning to achieve strong classification performance using fewer training samples. Specifically, the study compared EfficientNetV2 with its predecessor, EfficientNet, and with ResNet50 in classifying brain tumors into three types: glioma, meningioma, and pituitary tumors. Results showed that EfficientNetV2 delivered superior performance compared to the other models. However, this improvement came at the cost of increased training time, likely due to the model's greater complexity.

The circulation of cerebrospinal and interstitial fluid plays a vital role in clearing metabolic waste from the brain, and its disruption has been linked to neurological disorders. However, directly measuring brain-wide fluid transport-especially in the deep brain-has remained elusive. Here, we introduce magnetic resonance artificial intelligence velocimetry (MR-AIV), a framework featuring a specialized physics-informed architecture and optimization method that reconstructs three-dimensional fluid velocity fields from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). MR-AIV unveils brain-wide velocity maps while providing estimates of tissue permeability and pressure fields-quantities inaccessible to other methods. Applied to the brain, MR-AIV reveals a functional landscape of interstitial and perivascular flow, quantitatively distinguishing slow diffusion-driven transport (∼ 0.1 µm/s) from rapid advective flow (∼ 3 µm/s). This approach enables new investigations into brain clearance mechanisms and fluid dynamics in health and disease, with broad potential applications to other porous media systems, from geophysics to tissue mechanics.