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Profiling disease experience in patients living with brain aneurysms by analyzing multimodal clinical data and quality of life measures.

Reder SR, Hardt J, Brockmann MA, Brockmann C, Kim S, Kawulycz M, Schulz M, Kantelhardt SR, Petrowski K, Fischbeck S

pubmed logopapersAug 20 2025
To explore the mental and physical health (MH, PH) on individuals living with brain aneurysms and to profile their differences in disease experience. In N = 111 patients the Short Form 36 Health Survey (SF-36) was assessed via an online survey; Supplementary data included angiography and magnetic resonance imaging (MRI) findings (including AI-based brain Lesion Volume analyses in ml, or LV). Correlation and regression analyses were conducted (including biological sex, age, overall brain LV, PH, MH). Disease profiles were determined using principal component analysis. Compared to the German normative cohort, patients exhibited overall lower SF-36 scores. In regression analyses, the DW was predictable by PH (β = 0.345) and MH (β=-0.646; R = 0.557; p < 0.001). Vasospasm severity correlated significantly with LV (r = 0.242, p = 0.043), MH (r=-0.321, p = 0.043), and PH (r=-0.372, p = 0.028). Higher LV were associated with poorer PH (r=-0.502, p = 0.001), unlike MH (p > 0.05). Main disease profiles were identified: (1) those with increased LV post-rupture (high DW); (2) older individuals with stable aneurysms (low DW); (3) revealing a sex disparity in QoL despite similar vasospasm severity; and 4), focused on chronic pain and its impact on daily tasks. Two sub-profiles highlighted trauma-induced impairments, functional disabilities from LV, and persistent anxiety. Reduced thalamic and pallidal volumes were linked to low QoL following subarachnoid hemorrhage. MH has a greater impact on life quality compared to physical disabilities, leading to prolonged DW. A singular physical impairment was rather atypical for a perceived worse outcome. Patient profiles revealed that clinical history, sex, psychological stress, and pain each contribute uniquely to QoL and work capacity. Prioritizing MH in assessing workability and rehabilitation is crucial for survivors' long-term outcome.

Potential and challenges of generative adversarial networks for super-resolution in 4D Flow MRI

Oliver Welin Odeback, Arivazhagan Geetha Balasubramanian, Jonas Schollenberger, Edward Ferdiand, Alistair A. Young, C. Alberto Figueroa, Susanne Schnell, Outi Tammisola, Ricardo Vinuesa, Tobias Granberg, Alexander Fyrdahl, David Marlevi

arxiv logopreprintAug 20 2025
4D Flow Magnetic Resonance Imaging (4D Flow MRI) enables non-invasive quantification of blood flow and hemodynamic parameters. However, its clinical application is limited by low spatial resolution and noise, particularly affecting near-wall velocity measurements. Machine learning-based super-resolution has shown promise in addressing these limitations, but challenges remain, not least in recovering near-wall velocities. Generative adversarial networks (GANs) offer a compelling solution, having demonstrated strong capabilities in restoring sharp boundaries in non-medical super-resolution tasks. Yet, their application in 4D Flow MRI remains unexplored, with implementation challenged by known issues such as training instability and non-convergence. In this study, we investigate GAN-based super-resolution in 4D Flow MRI. Training and validation were conducted using patient-specific cerebrovascular in-silico models, converted into synthetic images via an MR-true reconstruction pipeline. A dedicated GAN architecture was implemented and evaluated across three adversarial loss functions: Vanilla, Relativistic, and Wasserstein. Our results demonstrate that the proposed GAN improved near-wall velocity recovery compared to a non-adversarial reference (vNRMSE: 6.9% vs. 9.6%); however, that implementation specifics are critical for stable network training. While Vanilla and Relativistic GANs proved unstable compared to generator-only training (vNRMSE: 8.1% and 7.8% vs. 7.2%), a Wasserstein GAN demonstrated optimal stability and incremental improvement (vNRMSE: 6.9% vs. 7.2%). The Wasserstein GAN further outperformed the generator-only baseline at low SNR (vNRMSE: 8.7% vs. 10.7%). These findings highlight the potential of GAN-based super-resolution in enhancing 4D Flow MRI, particularly in challenging cerebrovascular regions, while emphasizing the need for careful selection of adversarial strategies.

Multicenter Validation of Automated Segmentation and Composition Analysis of Lumbar Paraspinal Muscles Using Multisequence MRI.

Zhang Z, Hides JA, De Martino E, Millner J, Tuxworth G

pubmed logopapersAug 20 2025
<i>"Just Accepted" papers have undergone full peer review and have been accepted for publication in <i>Radiology: Artificial Intelligence</i>. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content</i>. Chronic low back pain is a global health issue with considerable socioeconomic burdens and is associated with changes in lumbar paraspinal muscles (LPM). In this retrospective study, a deep learning method was trained and externally validated for automated LPM segmentation, muscle volume quantification, and fatty infiltration assessment across multisequence MRIs. A total of 1,302 MRIs from 641 participants across five centers were included. Data from two centers were used for model training and tuning, while data from the remaining three centers were used for external testing. Model segmentation performance was evaluated against manual segmentation using the Dice similarity coefficient (DSC), and measurement accuracy was assessed using two one-sided tests and Intraclass Correlation Coefficients (ICCs). The model achieved global DSC values of 0.98 on the internal test set and 0.93 to 0.97 on external test sets. Statistical equivalence between automated and manual measurements of muscle volume and fat ratio was confirmed in most regions (<i>P</i> < .05). Agreement between automated and manual measurements was high (ICCs > 0.92). In conclusion, the proposed automated method accurately segmented LPM and demonstrated statistical equivalence to manual measurements of muscle volume and fatty infiltration ratio across multisequence, multicenter MRIs. ©RSNA, 2025.

An effective flowchart for multimodal brain tumor binary classification with ranked 3D texture features.

Barstuğan M

pubmed logopapersAug 20 2025
Brain tumors have complex structures, and their shape, density, and size can vary widely. Consequently, their accurate classification, which involves identifying features that best describe the tumor data, is challenging. Using classical 2D texture features can yield only limited accuracy. Here, we show that this limitation can be overcome by using 3D feature extraction and ranking methods. Brain tumor images obtained through 3D magnetic resonance imaging were used to classify high-grade and low-grade glioma in the BraTS 2017 dataset. From the dataset, texture properties for each of the four phases (i.e., FLAIR, T1, T1c, and T2) were extracted using a 3D gray level co-occurrence matrix. Various combinations of brain tumor feature sets were created, and feature ranking methods-Bhattacharyya, entropy, receiver operating characteristic, the t-test, and the Wilcoxon test-were applied to them. Features were classified using gradient boosting, support vector machines (SVMs), and random forest methods. The performance of all combinations was evaluated from the sensitivity, specificity, accuracy, precision, and F-score obtained from twofold, fivefold, and tenfold cross-validation tests. In all experiments, the most effective scheme was that involving the quadruple combination (FLAIR + T1 + T1c + T2) and the entropy feature-ranking method with twofold cross-validation. Notably, the proposed machine-learning-based framework showed remarkable scores of 100% (sensitivity), 97.29% (specificity), 99.30% (accuracy), 99.07% (precision), and 99.53% (F-score) for glioma classification with an SVM. The proposed flowchart reflects a novel brain tumor classification system that competes with the novel methods.

An MRI Atlas of the Human Fetal Brain: Reference and Segmentation Tools for Fetal Brain MRI Analysis

Mahdi Bagheri, Clemente Velasco-Annis, Jian Wang, Razieh Faghihpirayesh, Shadab Khan, Camilo Calixto, Camilo Jaimes, Lana Vasung, Abdelhakim Ouaalam, Onur Afacan, Simon K. Warfield, Caitlin K. Rollins, Ali Gholipour

arxiv logopreprintAug 20 2025
Accurate characterization of in-utero brain development is essential for understanding typical and atypical neurodevelopment. Building upon previous efforts to construct spatiotemporal fetal brain MRI atlases, we present the CRL-2025 fetal brain atlas, which is a spatiotemporal (4D) atlas of the developing fetal brain between 21 and 37 gestational weeks. This atlas is constructed from carefully processed MRI scans of 160 fetuses with typically-developing brains using a diffeomorphic deformable registration framework integrated with kernel regression on age. CRL-2025 uniquely includes detailed tissue segmentations, transient white matter compartments, and parcellation into 126 anatomical regions. This atlas offers significantly enhanced anatomical details over the CRL-2017 atlas, and is released along with the CRL diffusion MRI atlas with its newly created tissue segmentation and labels as well as deep learning-based multiclass segmentation models for fine-grained fetal brain MRI segmentation. The CRL-2025 atlas and its associated tools provide a robust and scalable platform for fetal brain MRI segmentation, groupwise analysis, and early neurodevelopmental research, and these materials are publicly released to support the broader research community.

Resilience and Brain Changes in Long-Term Ayahuasca Users: Insights From Psychometric and fMRI Pattern Recognition.

Ramos LR, Fernandes O, Sanchez TA

pubmed logopapersAug 20 2025
Ayahuasca is an Amazonian psychedelic brew that contains dimethyltryptamine (DMT) and beta carbolines. Prolonged use has shown changes in cognitive-behavioral tasks, and in humans, there is evidence of changes in cortical thickness and an increase in neuroplasticity factors that could lead to modifications in functional neural circuits. To investigate the long-term effects of Ayahuasca usage through psychometric scales and fMRI data related to emotional processing using artificial intelligence tools. Retrospective Cross-sectional, case-control study. 38 healthy male participants (19 long-term Ayahuasca users and 19 non-user controls). 1.5 Tesla; gradient-echo T2*-weighted echo-planar imaging sequence during an implicit emotion processing task. Participants completed standardized psychometric scales including the Ego Resilience Scale (ER89). During fMRI, participants performed a gender judgment task using faces with neutral or aversive (disgust/fear) expressions. Whole-brain fMRI data were analyzed using multivariate pattern recognition. Group comparisons of psychometric scores were performed using Student's t-tests or Mann-Whitney U tests based on normality. Multivariate pattern classification and regression were performed using machine learning algorithms: Multiple Kernel Learning (MKL), Support Vector Machine (SVM), and Gaussian Process Classification/Regression (GPC/GPR), with k-fold cross-validation and permutation testing (n = 100-1000) to assess model significance (α = 0.05). Ayahuasca users (mean = 43.89; SD = 5.64) showed significantly higher resilience scores compared to controls (mean = 39.05; SD = 5.34). The MKL classifier distinguished users from controls with 75% accuracy (p = 0.005). The GPR model significantly predicted individual resilience scores (r = 0.69). Long-term Ayahuasca use may be associated with altered emotional brain reactivity and increased psychological resilience. These findings support a neural patterns consistent with long-term adaptations of Ayahuasca detectable via fMRI and machine learning-based pattern analysis. 4. Stage 1.

Attention-based deep learning network for predicting World Health Organization meningioma grade and Ki-67 expression based on magnetic resonance imaging.

Cheng X, Li H, Li C, Li J, Liu Z, Fan X, Lu C, Song K, Shen Z, Wang Z, Yang Q, Zhang J, Yin J, Qian C, You Y, Wang X

pubmed logopapersAug 20 2025
Preoperative assessment of World Health Organization (WHO) meningioma grading and Ki-67 expression is crucial for treatment strategies. We aimed to develop a fully automated attention-based deep learning network to predict WHO meningioma grading and Ki-67 expression. This retrospective study included 952 meningioma patients, divided into training (n = 542), internal validation (n = 96), and external test sets (n = 314). For each task, clinical, radiomics, and deep learning models were compared. We used no-new-Unet (nn-Unet) models to construct the segmentation network, followed by four classification models using ResNet50 or Swin Transformer architectures with 2D or 2.5D input strategies. All deep learning models incorporated attention mechanisms. Both the segmentation and 2.5D classification models demonstrated robust performance on the external test set. The segmentation network achieved Dice coefficients of 0.98 (0.97-0.99) and 0.87 (0.83-0.91) for brain parenchyma and tumour segmentation. For predicting meningioma grade, the 2.5D ResNet50 achieved the highest area under the curve (AUC) of 0.90 (0.85-0.93), significantly outperforming the clinical (AUC = 0.77 [0.70-0.83], p < 0.001) and radiomics models (AUC = 0.80 [0.75-0.85], p < 0.001). For Ki-67 expression prediction, the 2.5D Swin Transformer achieved the highest AUC of 0.89 (0.85-0.93), outperforming both the clinical (AUC = 0.76 [0.71-0.81], p < 0.001) and radiomics models (AUC = 0.82 [0.77-0.86], p = 0.002). Our automated deep learning network demonstrated superior performance. This novel network could support more precise treatment planning for meningioma patients. Question Can artificial intelligence accurately assess meningioma WHO grade and Ki-67 expression from preoperative MRI to guide personalised treatment and follow-up strategies? Findings The attention-enhanced nn-Unet segmentation achieved high accuracy, while 2.5D deep learning models with attention mechanisms achieved accurate prediction of grades and Ki-67. Clinical relevance Our fully automated 2.5D deep learning model, enhanced with attention mechanisms, accurately predicts WHO grades and Ki-67 expression levels in meningiomas, offering a robust, objective, and non-invasive solution to support clinical diagnosis and optimise treatment planning.

AI-driven reclassification of multiple sclerosis progression.

Ganjgahi H, Häring DA, Aarden P, Graham G, Sun Y, Gardiner S, Su W, Berge C, Bischof A, Fisher E, Gaetano L, Thoma SP, Kieseier BC, Nichols TE, Thompson AJ, Montalban X, Lublin FD, Kappos L, Arnold DL, Bermel RA, Wiendl H, Holmes CC

pubmed logopapersAug 20 2025
Multiple sclerosis (MS) affects 2.9 million people. Traditional classification of MS into distinct subtypes poorly reflects its pathobiology and has limited value for prognosticating disease evolution and treatment response, thereby hampering drug discovery. Here we report a data-driven classification of MS disease evolution by analyzing a large clinical trial database (approximately 8,000 patients, 118,000 patient visits and more than 35,000 magnetic resonance imaging scans) using probabilistic machine learning. Four dimensions define MS disease states: physical disability, brain damage, relapse and subclinical disease activity. Early/mild/evolving (EME) MS and advanced MS represent two poles of a disease severity spectrum. Patients with EME MS show limited clinical impairment and minor brain damage. Transitions to advanced MS occur via brain damage accumulation through inflammatory states, with or without accompanying symptoms. Advanced MS is characterized by moderate to high disability levels, radiological disease burden and risk of disease progression independent of relapses, with little probability of returning to earlier MS states. We validated these results in an independent clinical trial database and a real-world cohort, totaling more than 4,000 patients with MS. Our findings support viewing MS as a disease continuum. We propose a streamlined disease classification to offer a unifying understanding of the disease, improve patient management and enhance drug discovery efficiency and precision.

Systematic Evaluation of Wavelet-Based Denoising for MRI Brain Images: Optimal Configurations and Performance Benchmarks

Asadullah Bin Rahman, Masud Ibn Afjal, Md. Abdulla Al Mamun

arxiv logopreprintAug 20 2025
Medical imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound are essential for accurate diagnosis and treatment planning in modern healthcare. However, noise contamination during image acquisition and processing frequently degrades image quality, obscuring critical diagnostic details and compromising clinical decision-making. Additionally, enhancement techniques such as histogram equalization may inadvertently amplify existing noise artifacts, including salt-and-pepper distortions. This study investigates wavelet transform-based denoising methods for effective noise mitigation in medical images, with the primary objective of identifying optimal combinations of threshold values, decomposition levels, and wavelet types to achieve superior denoising performance and enhanced diagnostic accuracy. Through systematic evaluation across various noise conditions, the research demonstrates that the bior6.8 biorthogonal wavelet with universal thresholding at decomposition levels 2-3 consistently achieves optimal denoising performance, providing significant noise reduction while preserving essential anatomical structures and diagnostic features critical for clinical applications.

Advanced liver fibrosis detection using a two-stage deep learning approach on standard T2-weighted MRI.

Gupta P, Singh S, Gulati A, Dutta N, Aggarwal Y, Kalra N, Premkumar M, Taneja S, Verma N, De A, Duseja A

pubmed logopapersAug 19 2025
To develop and validate a deep learning model for automated detection of advanced liver fibrosis using standard T2-weighted MRI. We utilized two datasets: the public CirrMRI600 + dataset (n = 374) containing T2-weighted MRI scans from patients with cirrhosis (n = 318) and healthy subjects (n = 56), and an in-house dataset of chronic liver disease patients (n = 187). A two-stage deep learning pipeline was developed: first, an automated liver segmentation model using nnU-Net architecture trained on CirrMRI600 + and then applied to segment livers in our in-house dataset; second, a Masked Attention ResNet classification model. For classification model training, patients with liver stiffness measurement (LSM) > 12 kPa were classified as advanced fibrosis (n = 104). In contrast, healthy subjects from CirrMRI600 + and patients with LSM ≤ 12 kPa were classified as non-advanced fibrosis (n = 116). Model validation was exclusively performed on a separate test set of 23 patients with histopathological confirmation of the degree of fibrosis (METAVIR ≥ F3 indicating advanced fibrosis). We additionally compared our two-stage approach with direct classification without segmentation, and evaluated alternative architectures including DenseNet121 and SwinTransformer. The liver segmentation model performed excellently on the test set (mean Dice score: 0.960 ± 0.009; IoU: 0.923 ± 0.016). On the pathologically confirmed independent test set (n = 23), our two-stage model achieved strong diagnostic performance (sensitivity: 0.778, specificity: 0.800, AUC: 0.811, accuracy: 0.783), significantly outperforming direct classification without segmentation (AUC: 0.743). Classification performance was highly dependent on segmentation quality, with cases having excellent segmentation (Score 1) showing higher accuracy (0.818) than those with poor segmentation (Score 3, accuracy: 0.625). Alternative architectures with masked attention showed comparable but slightly lower performance (DenseNet121: AUC 0.795; SwinTransformer: AUC 0.782). Our fully automated deep learning pipeline effectively detects advanced liver fibrosis using standard non-contrast T2-weighted MRI, potentially offering a non-invasive alternative to current diagnostic approaches. The segmentation-first approach provides significant performance gains over direct classification.
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