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How We Won the ISLES'24 Challenge by Preprocessing

Tianyi Ren, Juampablo E. Heras Rivera, Hitender Oswal, Yutong Pan, William Henry, Sophie Walters, Mehmet Kurt

arxiv logopreprintMay 23 2025
Stroke is among the top three causes of death worldwide, and accurate identification of stroke lesion boundaries is critical for diagnosis and treatment. Supervised deep learning methods have emerged as the leading solution for stroke lesion segmentation but require large, diverse, and annotated datasets. The ISLES'24 challenge addresses this need by providing longitudinal stroke imaging data, including CT scans taken on arrival to the hospital and follow-up MRI taken 2-9 days from initial arrival, with annotations derived from follow-up MRI. Importantly, models submitted to the ISLES'24 challenge are evaluated using only CT inputs, requiring prediction of lesion progression that may not be visible in CT scans for segmentation. Our winning solution shows that a carefully designed preprocessing pipeline including deep-learning-based skull stripping and custom intensity windowing is beneficial for accurate segmentation. Combined with a standard large residual nnU-Net architecture for segmentation, this approach achieves a mean test Dice of 28.5 with a standard deviation of 21.27.

Artificial Intelligence enhanced R1 maps can improve lesion detection in focal epilepsy in children

Doumou, G., D'Arco, F., Figini, M., Lin, H., Lorio, S., Piper, R., O'Muircheartaigh, J., Cross, H., Weiskopf, N., Alexander, D., Carmichael, D. W.

medrxiv logopreprintMay 23 2025
Background and purposeMRI is critical for the detection of subtle cortical pathology in epilepsy surgery assessment. This can be aided by improved MRI quality and resolution using ultra-high field (7T). But poor access and long scan durations limit widespread use, particularly in a paediatric setting. AI-based learning approaches may provide similar information by enhancing data obtained with conventional MRI (3T). We used a convolutional neural network trained on matched 3T and 7T images to enhance quantitative R1-maps (longitudinal relaxation rate) obtained at 3T in paediatric epilepsy patients and to determine their potential clinical value for lesion identification. Materials and MethodsA 3D U-Net was trained using paired patches from 3T and 7T R1-maps from n=10 healthy volunteers. The trained network was applied to enhance paediatric focal epilepsy 3T R1 images from a different scanner/site (n=17 MRI lesion positive / n=14 MR-negative). Radiological review assessed image quality, as well as lesion identification and visualization of enhanced maps in comparison to the 3T R1-maps without clinical information. Lesion appearance was then compared to 3D-FLAIR. ResultsAI enhanced R1 maps were superior in terms of image quality in comparison to the original 3T R1 maps, while preserving and enhancing the visibility of lesions. After exclusion of 5/31 patients (due to movement artefact or incomplete data), lesions were detected in AI Enhanced R1 maps for 14/15 (93%) MR-positive and 4/11 (36%) MR-negative patients. ConclusionAI enhanced R1 maps improved the visibility of lesions in MR positive patients, as well as providing higher sensitivity in the MR-negative group compared to either the original 3T R1-maps or 3D-FLAIR. This provides promising initial evidence that 3T quantitative maps can outperform conventional 3T imaging via enhancement by an AI model trained on 7T MRI data, without the need for pathology-specific information.

Brain age prediction from MRI scans in neurodegenerative diseases.

Papouli A, Cole JH

pubmed logopapersMay 22 2025
This review explores the use of brain age estimation from MRI scans as a biomarker of brain health. With disorders like Alzheimer's and Parkinson's increasing globally, there is an urgent need for early detection tools that can identify at-risk individuals before cognitive symptoms emerge. Brain age offers a noninvasive, quantitative measure of neurobiological ageing, with applications in early diagnosis, disease monitoring, and personalized medicine. Studies show that individuals with Alzheimer's, mild cognitive impairment (MCI), and Parkinson's have older brain ages than their chronological age. Longitudinal research indicates that brain-predicted age difference (brain-PAD) rises with disease progression and often precedes cognitive decline. Advances in deep learning and multimodal imaging have improved the accuracy and interpretability of brain age predictions. Moreover, socioeconomic disparities and environmental factors significantly affect brain aging, highlighting the need for inclusive models. Brain age estimation is a promising biomarker for identify future risk of neurodegenerative disease, monitoring progression, and helping prognosis. Challenges like implementation of standardization, demographic biases, and interpretability remain. Future research should integrate brain age with biomarkers and multimodal imaging to enhance early diagnosis and intervention strategies.

Mitigating Overfitting in Medical Imaging: Self-Supervised Pretraining vs. ImageNet Transfer Learning for Dermatological Diagnosis

Iván Matas, Carmen Serrano, Miguel Nogales, David Moreno, Lara Ferrándiz, Teresa Ojeda, Begoña Acha

arxiv logopreprintMay 22 2025
Deep learning has transformed computer vision but relies heavily on large labeled datasets and computational resources. Transfer learning, particularly fine-tuning pretrained models, offers a practical alternative; however, models pretrained on natural image datasets such as ImageNet may fail to capture domain-specific characteristics in medical imaging. This study introduces an unsupervised learning framework that extracts high-value dermatological features instead of relying solely on ImageNet-based pretraining. We employ a Variational Autoencoder (VAE) trained from scratch on a proprietary dermatological dataset, allowing the model to learn a structured and clinically relevant latent space. This self-supervised feature extractor is then compared to an ImageNet-pretrained backbone under identical classification conditions, highlighting the trade-offs between general-purpose and domain-specific pretraining. Our results reveal distinct learning patterns. The self-supervised model achieves a final validation loss of 0.110 (-33.33%), while the ImageNet-pretrained model stagnates at 0.100 (-16.67%), indicating overfitting. Accuracy trends confirm this: the self-supervised model improves from 45% to 65% (+44.44%) with a near-zero overfitting gap, whereas the ImageNet-pretrained model reaches 87% (+50.00%) but plateaus at 75% (+19.05%), with its overfitting gap increasing to +0.060. These findings suggest that while ImageNet pretraining accelerates convergence, it also amplifies overfitting on non-clinically relevant features. In contrast, self-supervised learning achieves steady improvements, stronger generalization, and superior adaptability, underscoring the importance of domain-specific feature extraction in medical imaging.

FLAMeS: A Robust Deep Learning Model for Automated Multiple Sclerosis Lesion Segmentation

Dereskewicz, E., La Rosa, F., dos Santos Silva, J., Sizer, E., Kohli, A., Wynen, M., Mullins, W. A., Maggi, P., Levy, S., Onyemeh, K., Ayci, B., Solomon, A. J., Assländer, J., Al-Louzi, O., Reich, D. S., Sumowski, J. F., Beck, E. S.

medrxiv logopreprintMay 22 2025
Background and Purpose Assessment of brain lesions on MRI is crucial for research in multiple sclerosis (MS). Manual segmentation is time consuming and inconsistent. We aimed to develop an automated MS lesion segmentation algorithm for T2-weighted fluid-attenuated inversion recovery (FLAIR) MRI. Methods We developed FLAIR Lesion Analysis in Multiple Sclerosis (FLAMeS), a deep learning-based MS lesion segmentation algorithm based on the nnU-Net 3D full-resolution U-Net and trained on 668 FLAIR 1.5 and 3 tesla scans from persons with MS. FLAMeS was evaluated on three external datasets: MSSEG-2 (n=14), MSLesSeg (n=51), and a clinical cohort (n=10), and compared to SAMSEG, LST-LPA, and LST-AI. Performance was assessed qualitatively by two blinded experts and quantitatively by comparing automated and ground truth lesion masks using standard segmentation metrics. Results In a blinded qualitative review of 20 scans, both raters selected FLAMeS as the most accurate segmentation in 15 cases, with one rater favoring FLAMeS in two additional cases. Across all testing datasets, FLAMeS achieved a mean Dice score of 0.74, a true positive rate of 0.84, and an F1 score of 0.78, consistently outperforming the benchmark methods. For other metrics, including positive predictive value, relative volume difference, and false positive rate, FLAMeS performed similarly or better than benchmark methods. Most lesions missed by FLAMeS were smaller than 10 mm3, whereas the benchmark methods missed larger lesions in addition to smaller ones. Conclusions FLAMeS is an accurate, robust method for MS lesion segmentation that outperforms other publicly available methods.

Radiomics-Based Early Triage of Prostate Cancer: A Multicenter Study from the CHAIMELEON Project

Vraka, A., Marfil-Trujillo, M., Ribas-Despuig, G., Flor-Arnal, S., Cerda-Alberich, L., Jimenez-Gomez, P., Jimenez-Pastor, A., Marti-Bonmati, L.

medrxiv logopreprintMay 22 2025
Prostate cancer (PCa) is the most commonly diagnosed malignancy in men worldwide. Accurate triage of patients based on tumor aggressiveness and staging is critical for selecting appropriate management pathways. While magnetic resonance imaging (MRI) has become a mainstay in PCa diagnosis, most predictive models rely on multiparametric imaging or invasive inputs, limiting generalizability in real-world clinical settings. This study aimed to develop and validate machine learning (ML) models using radiomic features extracted from T2-weighted MRI--alone and in combination with clinical variables--to predict ISUP grade (tumor aggressiveness), lymph node involvement (cN) and distant metastasis (cM). A retrospective multicenter cohort from three European sites in the Chaimeleon project was analyzed. Radiomic features were extracted from prostate zone segmentations and lesion masks, following standardized preprocessing and ComBat harmonization. Feature selection and model optimization were performed using nested cross-validation and Bayesian tuning. Hybrid models were trained using XGBoost and interpreted with SHAP values. The ISUP model achieved an AUC of 0.66, while the cN and cM models reached AUCs of 0.77 and 0.80, respectively. The best-performing models consistently combined prostate zone radiomics with clinical features such as PSA, PIRADSv2 and ISUP grade. SHAP analysis confirmed the importance of both clinical and texture-based radiomic features, with entropy and non-uniformity measures playing central roles in all tasks. Our results demonstrate the feasibility of using T2-weighted MRI and zonal radiomics for robust prediction of aggressiveness, nodal involvement and distant metastasis in PCa. This fully automated pipeline offers an interpretable, accessible and clinically translatable tool for first-line PCa triage, with potential integration into real-world diagnostic workflows.

Patient Reactions to Artificial Intelligence-Clinician Discrepancies: Web-Based Randomized Experiment.

Madanay F, O'Donohue LS, Zikmund-Fisher BJ

pubmed logopapersMay 22 2025
As the US Food and Drug Administration (FDA)-approved use of artificial intelligence (AI) for medical imaging rises, radiologists are increasingly integrating AI into their clinical practices. In lung cancer screening, diagnostic AI offers a second set of eyes with the potential to detect cancer earlier than human radiologists. Despite AI's promise, a potential problem with its integration is the erosion of patient confidence in clinician expertise when there is a discrepancy between the radiologist's and the AI's interpretation of the imaging findings. We examined how discrepancies between AI-derived recommendations and radiologists' recommendations affect patients' agreement with radiologists' recommendations and satisfaction with their radiologists. We also analyzed how patients' medical maximizing-minimizing preferences moderate these relationships. We conducted a randomized, between-subjects experiment with 1606 US adult participants. Assuming the role of patients, participants imagined undergoing a low-dose computerized tomography scan for lung cancer screening and receiving results and recommendations from (1) a radiologist only, (2) AI and a radiologist in agreement, (3) a radiologist who recommended more testing than AI (ie, radiologist overcalled AI), or (4) a radiologist who recommended less testing than AI (ie, radiologist undercalled AI). Participants rated the radiologist on three criteria: agreement with the radiologist's recommendation, how likely they would be to recommend the radiologist to family and friends, and how good of a provider they perceived the radiologist to be. We measured medical maximizing-minimizing preferences and categorized participants as maximizers (ie, those who seek aggressive intervention), minimizers (ie, those who prefer no or passive intervention), and neutrals (ie, those in the middle). Participants' agreement with the radiologist's recommendation was significantly lower when the radiologist undercalled AI (mean 4.01, SE 0.07, P<.001) than in the other 3 conditions, with no significant differences among them (radiologist overcalled AI [mean 4.63, SE 0.06], agreed with AI [mean 4.55, SE 0.07], or had no AI [mean 4.57, SE 0.06]). Similarly, participants were least likely to recommend (P<.001) and positively rate (P<.001) the radiologist who undercalled AI, with no significant differences among the other conditions. Maximizers agreed with the radiologist who overcalled AI (β=0.82, SE 0.14; P<.001) and disagreed with the radiologist who undercalled AI (β=-0.47, SE 0.14; P=.001). However, whereas minimizers disagreed with the radiologist who overcalled AI (β=-0.43, SE 0.18, P=.02), they did not significantly agree with the radiologist who undercalled AI (β=0.14, SE 0.17, P=.41). Radiologists who recommend less testing than AI may face decreased patient confidence in their expertise, but they may not face this same penalty for giving more aggressive recommendations than AI. Patients' reactions may depend in part on whether their general preferences to maximize or minimize align with the radiologists' recommendations. Future research should test communication strategies for radiologists' disclosure of AI discrepancies to patients.

A Novel Dynamic Neural Network for Heterogeneity-Aware Structural Brain Network Exploration and Alzheimer's Disease Diagnosis.

Cui W, Leng Y, Peng Y, Bai C, Li L, Jiang X, Yuan G, Zheng J

pubmed logopapersMay 22 2025
Heterogeneity is a fundamental characteristic of brain diseases, distinguished by variability not only in brain atrophy but also in the complexity of neural connectivity and brain networks. However, existing data-driven methods fail to provide a comprehensive analysis of brain heterogeneity. Recently, dynamic neural networks (DNNs) have shown significant advantages in capturing sample-wise heterogeneity. Therefore, in this article, we first propose a novel dynamic heterogeneity-aware network (DHANet) to identify critical heterogeneous brain regions, explore heterogeneous connectivity between them, and construct a heterogeneous-aware structural brain network (HGA-SBN) using structural magnetic resonance imaging (sMRI). Specifically, we develop a 3-D dynamic convmixer to extract abundant heterogeneous features from sMRI first. Subsequently, the critical brain atrophy regions are identified by dynamic prototype learning with embedding the hierarchical brain semantic structure. Finally, we employ a joint dynamic edge-correlation (JDE) modeling approach to construct the heterogeneous connectivity between these regions and analyze the HGA-SBN. To evaluate the effectiveness of the DHANet, we conduct elaborate experiments on three public datasets and the method achieves state-of-the-art (SOTA) performance on two classification tasks.

Cross-Scale Texture Supplementation for Reference-based Medical Image Super-Resolution.

Li Y, Hao W, Zeng H, Wang L, Xu J, Routray S, Jhaveri RH, Gadekallu TR

pubmed logopapersMay 22 2025
Magnetic Resonance Imaging (MRI) is a widely used medical imaging technique, but its resolution is often limited by acquisition time constraints, potentially compromising diagnostic accuracy. Reference-based Image Super-Resolution (RefSR) has shown promising performance in addressing such challenges by leveraging external high-resolution (HR) reference images to enhance the quality of low-resolution (LR) images. The core objective of RefSR is to accurately establish correspondences between the reference HR image and the LR images. In pursuit of this objective, this paper develops a Self-rectified Texture Supplementation network for RefSR (STS-SR) to enhance fine details in MRI images and support the expanding role of autonomous AI in healthcare. Our network comprises a texture-specified selfrectified feature transfer module and a cross-scale texture complementary network. The feature transfer module employs highfrequency filtering to facilitate the network concentrating on fine details. To better exploit the information from both the reference and LR images, our cross-scale texture complementary module incorporates the All-ViT and Swin Transformer layers to achieve feature aggregation at multiple scales, which enables high-quality image enhancement that is critical for autonomous AI systems in healthcare to make accurate decisions. Extensive experiments are performed across various benchmark datasets. The results validate the effectiveness of our method and demonstrate that the method produces state-of-the-art performance as compared to existing approaches. This advancement enables autonomous AI systems to utilize high-quality MRI images for more accurate diagnostics and reliable predictions.

HealthiVert-GAN: A Novel Framework of Pseudo-Healthy Vertebral Image Synthesis for Interpretable Compression Fracture Grading.

Zhang Q, Chuang C, Zhang S, Zhao Z, Wang K, Xu J, Sun J

pubmed logopapersMay 22 2025
Osteoporotic vertebral compression fractures (OVCFs) are prevalent in the elderly population, typically assessed on computed tomography (CT) scans by evaluating vertebral height loss. This assessment helps determine the fracture's impact on spinal stability and the need for surgical intervention. However, the absence of pre-fracture CT scans and standardized vertebral references leads to measurement errors and inter-observer variability, while irregular compression patterns further challenge the precise grading of fracture severity. While deep learning methods have shown promise in aiding OVCFs screening, they often lack interpretability and sufficient sensitivity, limiting their clinical applicability. To address these challenges, we introduce a novel vertebra synthesis-height loss quantification-OVCFs grading framework. Our proposed model, HealthiVert-GAN, utilizes a coarse-to-fine synthesis network designed to generate pseudo-healthy vertebral images that simulate the pre-fracture state of fractured vertebrae. This model integrates three auxiliary modules that leverage the morphology and height information of adjacent healthy vertebrae to ensure anatomical consistency. Additionally, we introduce the Relative Height Loss of Vertebrae (RHLV) as a quantification metric, which divides each vertebra into three sections to measure height loss between pre-fracture and post-fracture states, followed by fracture severity classification using a Support Vector Machine (SVM). Our approach achieves state-of-the-art classification performance on both the Verse2019 dataset and in-house dataset, and it provides cross-sectional distribution maps of vertebral height loss. This practical tool enhances diagnostic accuracy in clinical settings and assisting in surgical decision-making.
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