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Integrating Radiomics with Deep Learning Enhances Multiple Sclerosis Lesion Delineation

Nadezhda Alsahanova, Pavel Bartenev, Maksim Sharaev, Milos Ljubisavljevic, Taleb Al. Mansoori, Yauhen Statsenko

arxiv logopreprintJun 17 2025
Background: Accurate lesion segmentation is critical for multiple sclerosis (MS) diagnosis, yet current deep learning approaches face robustness challenges. Aim: This study improves MS lesion segmentation by combining data fusion and deep learning techniques. Materials and Methods: We suggested novel radiomic features (concentration rate and R\'enyi entropy) to characterize different MS lesion types and fused these with raw imaging data. The study integrated radiomic features with imaging data through a ResNeXt-UNet architecture and attention-augmented U-Net architecture. Our approach was evaluated on scans from 46 patients (1102 slices), comparing performance before and after data fusion. Results: The radiomics-enhanced ResNeXt-UNet demonstrated high segmentation accuracy, achieving significant improvements in precision and sensitivity over the MRI-only baseline and a Dice score of 0.774$\pm$0.05; p<0.001 according to Bonferroni-adjusted Wilcoxon signed-rank tests. The radiomics-enhanced attention-augmented U-Net model showed a greater model stability evidenced by reduced performance variability (SDD = 0.18 $\pm$ 0.09 vs. 0.21 $\pm$ 0.06; p=0.03) and smoother validation curves with radiomics integration. Conclusion: These results validate our hypothesis that fusing radiomics with raw imaging data boosts segmentation performance and stability in state-of-the-art models.

Application of Convolutional Neural Network Denoising to Improve Cone Beam CT Myelographic Images.

Madhavan AA, Zhou Z, Thorne J, Kodet ML, Cutsforth-Gregory JK, Schievink WI, Mark IT, Schueler BA, Yu L

pubmed logopapersJun 17 2025
Cone beam CT is an imaging modality that provides high-resolution, cross-sectional imaging in the fluoroscopy suite. In neuroradiology, cone beam CT has been used for various applications including temporal bone imaging and during spinal and cerebral angiography. Furthermore, cone beam CT has been shown to improve imaging of spinal CSF leaks during myelography. One drawback of cone beam CT is that images have a relatively high noise level. In this technical report, we describe the first application of a high-resolution convolutional neural network to denoise cone beam CT myelographic images. We show examples of the resulting improvement in image quality for a variety of types of spinal CSF leaks. Further application of this technique is warranted to demonstrate its clinical utility and potential use for other cone beam CT applications.ABBREVIATIONS: CBCT = cone beam CT; CB-CTM = cone beam CT myelography; CTA = CT angiography; CVF = CSF-venous fistula; DSM = digital subtraction myelography; EID = energy integrating detector; FBP = filtered back-projection; SNR = signal-to-noise ratio.

A Robust Residual Three-dimensional Convolutional Neural Networks Model for Prediction of Amyloid-β Positivity by Using FDG-PET.

Ardakani I, Yamada T, Iwano S, Kumar Maurya S, Ishii K

pubmed logopapersJun 17 2025
Widely used in oncology PET, 2-deoxy-2-18F-FDG PET is more accessible and affordable than amyloid PET, which is a crucial tool to determine amyloid positivity in diagnosis of Alzheimer disease (AD). This study aimed to leverage deep learning with residual 3D convolutional neural networks (3DCNN) to develop a robust model that predicts amyloid-β positivity by using FDG-PET. In this study, a cohort of 187 patients was used for model development. It consisted of patients ranging from cognitively normal to those with dementia and other cognitive impairments who underwent T1-weighted MRI, 18F-FDG, and 11C-Pittsburgh compound B (PiB) PET scans. A residual 3DCNN model was configured using nonexhaustive grid search and trained on repeated random splits of our development data set. We evaluated the performance of our model, and particularly its robustness, using a multisite data set of 99 patients of different ethnicities with images at different site harmonization levels. Our model achieved mean AUC scores of 0.815 and 0.840 on images without and with site harmonization correspondingly. Respectively, it achieved higher AUC scores of 0.801 and 0.834 in the cognitively normal (CN) group compared with 0.777 and 0.745 in the dementia group. As for F1 score, the corresponding mean scores were 0.770 and 0.810 on images without and with site harmonization. In the CN group, it achieved lower F1 scores of 0.580 and 0.658 compared with 0.907 and 0.931 in the dementia group. We demonstrated that residual 3DCNN can learn complex 3D spatial patterns in FDG-PET images and robustly predict amyloid-β positivity with significantly less reliance on site harmonization preprocessing.

Transformer-augmented lightweight U-Net (UAAC-Net) for accurate MRI brain tumor segmentation.

Varghese NE, John A, C UDA, Pillai MJ

pubmed logopapersJun 17 2025
Accurate segmentation of brain tumor images, particularly gliomas in MRI scans, is crucial for early diagnosis, monitoring progression, and evaluating tumor structure and therapeutic response. A novel lightweight, transformer-based U-Net model for brain tumor segmentation, integrating attention mechanisms and multi-layer feature extraction via atrous convolution to capture long-range relationships and contextual information across image regions is proposed in this work. The model performance is evaluated on the publicly accessible BraTS 2020 dataset using evaluation metrics such as the Dice coefficient, accuracy, mean Intersection over Union (IoU), sensitivity, and specificity. The proposed model outperforms many of the existing methods, such as MimicNet, Swin Transformer-based UNet and hybrid multiresolution-based UNet, and is capable of handling a variety of segmentation issues. The experimental results demonstrate that the proposed model acheives an accuracy of 98.23%, a Dice score of 0.9716, and a mean IoU of 0.8242 during training when compared to the current state-of-the-art methods.

Enhancing cerebral infarct classification by automatically extracting relevant fMRI features.

Dobromyslin VI, Zhou W

pubmed logopapersJun 17 2025
Accurate detection of cortical infarct is critical for timely treatment and improved patient outcomes. Current brain imaging methods often require invasive procedures that primarily assess blood vessel and structural white matter damage. There is a need for non-invasive approaches, such as functional MRI (fMRI), that better reflect neuronal viability. This study utilized automated machine learning (auto-ML) techniques to identify novel infarct-specific fMRI biomarkers specifically related to chronic cortical infarcts. We analyzed resting-state fMRI data from the multi-center ADNI dataset, which included 20 chronic infarct patients and 30 cognitively normal (CN) controls. This study utilized automated machine learning (auto-ML) techniques to identify novel fMRI biomarkers specifically related to chronic cortical infarcts. Surface-based registration methods were applied to minimize partial-volume effects typically associated with lower resolution fMRI data. We evaluated the performance of 7 previously known fMRI biomarkers alongside 107 new auto-generated fMRI biomarkers across 33 different classification models. Our analysis identified 6 new fMRI biomarkers that substantially improved infarct detection performance compared to previously established metrics. The best-performing combination of biomarkers and classifiers achieved a cross-validation ROC score of 0.791, closely matching the accuracy of diffusion-weighted imaging methods used in acute stroke detection. Our proposed auto-ML fMRI infarct-detection technique demonstrated robustness across diverse imaging sites and scanner types, highlighting the potential of automated feature extraction to significantly enhance non-invasive infarct detection.

Exploring factors driving the evolution of chronic lesions in multiple sclerosis using machine learning.

Hu H, Ye L, Wu P, Shi Z, Chen G, Li Y

pubmed logopapersJun 17 2025
The study aimed to identify factors influencing the evolution of chronic lesions in multiple sclerosis (MS) using a machine learning approach. Longitudinal data were collected from individuals with relapsing-remitting multiple sclerosis (RRMS). The "iron rim" sign was identified using quantitative susceptibility mapping (QSM), and microstructural damage was quantified via T1/fluid attenuated inversion recovery (FLAIR) ratios. Additional data included baseline lesion volume, cerebral T2-hyperintense lesion volume, iron rim lesion volume, the proportion of iron rim lesion volume, gender, age, disease duration (DD), disability and cognitive scores, use of disease-modifying therapy, and follow-up intervals. These features were integrated into machine learning models (logistic regression (LR), random forest (RF), and support vector machine (SVM)) to predict lesion volume change, with the most predictive model selected for feature importance analysis. The study included 47 RRMS individuals (mean age, 30.6 ± 8.0 years [standard deviation], 6 males) and 833 chronic lesions. Machine learning model development results showed that the SVM model demonstrated superior predictive efficiency, with an AUC of 0.90 in the training set and 0.81 in the testing set. Feature importance analysis identified the top three features were the "iron rim" sign of lesions, DD, and the T1/FLAIR ratios of the lesions. This study developed a machine learning model to predict the volume outcome of MS lesions. Feature importance analysis identified chronic inflammation around the lesion, DD, and the microstructural damage as key factors influencing volume change in chronic MS lesions. Question The evolution of different chronic lesions in MS exhibits variability, and the driving factors influencing these outcomes remain to be further investigated. Findings A SVM learning model was developed to predict chronic MS lesion volume changes, integrating lesion characteristics, lesion burden, and clinical data. Clinical relevance Chronic inflammation surrounding lesions, DD, and microstructural damage are key factors influencing the evolution of chronic MS lesions.

Think deep in the tractography game: deep learning for tractography computing and analysis.

Zhang F, Théberge A, Jodoin PM, Descoteaux M, O'Donnell LJ

pubmed logopapersJun 16 2025
Tractography is a challenging process with complex rules, driving continuous algorithmic evolution to address its challenges. Meanwhile, deep learning has tackled similarly difficult tasks, such as mastering the Go board game and animating sophisticated robots. Given its transformative impact in these areas, deep learning has the potential to revolutionize tractography within the framework of existing rules. This work provides a brief summary of recent advances and challenges in deep learning-based tractography computing and analysis.

Radiologist-AI workflow can be modified to reduce the risk of medical malpractice claims

Bernstein, M., Sheppard, B., Bruno, M. A., Lay, P. S., Baird, G. L.

medrxiv logopreprintJun 16 2025
BackgroundArtificial Intelligence (AI) is rapidly changing the legal landscape of radiology. Results from a previous experiment suggested that providing AI error rates can reduce perceived radiologist culpability, as judged by mock jury members (4). The current study advances this work by examining whether the radiologists behavior also impacts perceptions of liability. Methods. Participants (n=282) read about a hypothetical malpractice case where a 50-year-old who visited the Emergency Department with acute neurological symptoms received a brain CT scan to determine if bleeding was present. An AI system was used by the radiologist who interpreted imaging. The AI system correctly flagged the case as abnormal. Nonetheless, the radiologist concluded no evidence of bleeding, and the blood-thinner t-PA was administered. Participants were randomly assigned to either a 1.) single-read condition, where the radiologist interpreted the CT once after seeing AI feedback, or 2.) a double-read condition, where the radiologist interpreted the CT twice, first without AI and then with AI feedback. Participants were then told the patient suffered irreversible brain damage due to the missed brain bleed, resulting in the patient (plaintiff) suing the radiologist (defendant). Participants indicated whether the radiologist met their duty of care to the patient (yes/no). Results. Hypothetical jurors were more likely to side with the plaintiff in the single-read condition (106/142, 74.7%) than in the double-read condition (74/140, 52.9%), p=0.0002. Conclusion. This suggests that the penalty for disagreeing with correct AI can be mitigated when images are interpreted twice, or at least if a radiologist gives an interpretation before AI is used.

Rate of brain aging associates with future executive function in Asian children and older adults.

Cheng SF, Yue WL, Ng KK, Qian X, Liu S, Tan TWK, Nguyen KN, Leong RLF, Hilal S, Cheng CY, Tan AP, Law EC, Gluckman PD, Chen CL, Chong YS, Meaney MJ, Chee MWL, Yeo BTT, Zhou JH

pubmed logopapersJun 16 2025
Brain age has emerged as a powerful tool to understand neuroanatomical aging and its link to health outcomes like cognition. However, there remains a lack of studies investigating the rate of brain aging and its relationship to cognition. Furthermore, most brain age models are trained and tested on cross-sectional data from primarily Caucasian, adult participants. It is thus unclear how well these models generalize to non-Caucasian participants, especially children. Here, we tested a previously published deep learning model on Singaporean elderly participants (55-88 years old) and children (4-11 years old). We found that the model directly generalized to the elderly participants, but model finetuning was necessary for children. After finetuning, we found that the rate of change in brain age gap was associated with future executive function performance in both elderly participants and children. We further found that lateral ventricles and frontal areas contributed to brain age prediction in elderly participants, while white matter and posterior brain regions were more important in predicting brain age of children. Taken together, our results suggest that there is potential for generalizing brain age models to diverse populations. Moreover, the longitudinal change in brain age gap reflects developing and aging processes in the brain, relating to future cognitive function.

Kernelized weighted local information based picture fuzzy clustering with multivariate coefficient of variation and modified total Bregman divergence measure for brain MRI image segmentation.

Lohit H, Kumar D

pubmed logopapersJun 16 2025
This paper proposes a novel clustering method for noisy image segmentation using a kernelized weighted local information approach under the Picture Fuzzy Set (PFS) framework. Existing kernel-based fuzzy clustering methods struggle with noisy environments and non-linear structures, while intuitionistic fuzzy clustering methods face limitations in handling uncertainty in real-world medical images. To address these challenges, we introduce a local picture fuzzy information measure, developed for the first time using Multivariate Coefficient of Variation (MCV) theory, enhancing robustness in segmentation. Additionally, we integrate non-Euclidean distance measures, including kernel distance for local information computation and modified total Bregman divergence (MTBD) measure for improving clustering accuracy. This combination enhances both local spatial consistency and global membership estimation, leading to precise segmentation. The proposed method is extensively evaluated on synthetic images with Gaussian, Salt and Pepper, and mixed noise, along with Brainweb, IBSR, and MRBrainS18 MRI datasets under varying Rician noise levels, and a CT image template. Furthermore, we benchmark our proposed method against two deep learning-based segmentation models, ResNet34-LinkNet and patch-based U-Net. Experimental results demonstrate significant improvements in segmentation accuracy, as validated by metrics such as Dice Score, Fuzzy Performance Index, Modified Partition Entropy, Average Volume Difference (AVD), and the XB index. Additionally, Friedman's statistical test confirms the superior performance of our approach compared to state-of-the-art clustering methods for noisy image segmentation. To facilitate reproducibility, the implementation of our proposed method is made publicly available at: Google Drive Repository.
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