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End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images

Jesper Duemose Nielsen, Karthik Gopinath, Andrew Hoopes, Adrian Dalca, Colin Magdamo, Steven Arnold, Sudeshna Das, Axel Thielscher, Juan Eugenio Iglesias, Oula Puonti

arxiv logopreprintMay 20 2025
Surface-based cortical analysis is valuable for a variety of neuroimaging tasks, such as spatial normalization, parcellation, and gray matter (GM) thickness estimation. However, most tools for estimating cortical surfaces work exclusively on scans with at least 1 mm isotropic resolution and are tuned to a specific magnetic resonance (MR) contrast, often T1-weighted (T1w). This precludes application using most clinical MR scans, which are very heterogeneous in terms of contrast and resolution. Here, we use synthetic domain-randomized data to train the first neural network for explicit estimation of cortical surfaces from scans of any contrast and resolution, without retraining. Our method deforms a template mesh to the white matter (WM) surface, which guarantees topological correctness. This mesh is further deformed to estimate the GM surface. We compare our method to recon-all-clinical (RAC), an implicit surface reconstruction method which is currently the only other tool capable of processing heterogeneous clinical MR scans, on ADNI and a large clinical dataset (n=1,332). We show a approximately 50 % reduction in cortical thickness error (from 0.50 to 0.24 mm) with respect to RAC and better recovery of the aging-related cortical thinning patterns detected by FreeSurfer on high-resolution T1w scans. Our method enables fast and accurate surface reconstruction of clinical scans, allowing studies (1) with sample sizes far beyond what is feasible in a research setting, and (2) of clinical populations that are difficult to enroll in research studies. The code is publicly available at https://github.com/simnibs/brainnet.

TransMedSeg: A Transferable Semantic Framework for Semi-Supervised Medical Image Segmentation

Mengzhu Wang, Jiao Li, Shanshan Wang, Long Lan, Huibin Tan, Liang Yang, Guoli Yang

arxiv logopreprintMay 20 2025
Semi-supervised learning (SSL) has achieved significant progress in medical image segmentation (SSMIS) through effective utilization of limited labeled data. While current SSL methods for medical images predominantly rely on consistency regularization and pseudo-labeling, they often overlook transferable semantic relationships across different clinical domains and imaging modalities. To address this, we propose TransMedSeg, a novel transferable semantic framework for semi-supervised medical image segmentation. Our approach introduces a Transferable Semantic Augmentation (TSA) module, which implicitly enhances feature representations by aligning domain-invariant semantics through cross-domain distribution matching and intra-domain structural preservation. Specifically, TransMedSeg constructs a unified feature space where teacher network features are adaptively augmented towards student network semantics via a lightweight memory module, enabling implicit semantic transformation without explicit data generation. Interestingly, this augmentation is implicitly realized through an expected transferable cross-entropy loss computed over the augmented teacher distribution. An upper bound of the expected loss is theoretically derived and minimized during training, incurring negligible computational overhead. Extensive experiments on medical image datasets demonstrate that TransMedSeg outperforms existing semi-supervised methods, establishing a new direction for transferable representation learning in medical image analysis.

Deep learning-based radiomics and machine learning for prognostic assessment in IDH-wildtype glioblastoma after maximal safe surgical resection: a multicenter study.

Liu J, Jiang S, Wu Y, Zou R, Bao Y, Wang N, Tu J, Xiong J, Liu Y, Li Y

pubmed logopapersMay 20 2025
Glioblastoma (GBM) is a highly aggressive brain tumor with poor prognosis. This study aimed to construct and validate a radiomics-based machine learning model for predicting overall survival (OS) in IDH-wildtype GBM after maximal safe surgical resection using magnetic resonance imaging. A total of 582 patients were retrospectively enrolled, comprising 301 in the training cohort, 128 in the internal validation cohort, and 153 in the external validation cohort. Volumes of interest (VOIs) from contrast-enhanced T1-weighted imaging (CE-T1WI) were segmented into three regions: contrast-enhancing tumor, necrotic non-enhancing core, and peritumoral edema using an ResNet-based segmentation network. A total of 4,227 radiomic features were extracted and filtered using LASSO-Cox regression to identify signatures. The prognostic model was constructed using the Mime prediction framework, categorizing patients into high- and low-risk groups based on the median OS. Model performance was assessed using the concordance index (CI) and Kaplan-Meier survival analysis. Independent prognostic factors were identified through multivariable Cox regression analysis, and a nomogram was developed for individualized risk assessment. The Step Cox [backward] + RSF model achieved CIs of 0.89, 0.81, and 0.76 in the training, internal and external validation cohorts. Log-rank tests demonstrated significant survival differences between high- and low-risk groups across all cohorts (P < 0.05). Multivariate Cox analysis identified age (HR: 1.022; 95% CI: 0.979, 1.009, P < 0.05), KPS score (HR: 0.970, 95% CI: 0.960, 0.978, P < 0.05), rad-scores of the necrotic non-enhancing core (HR: 8.164; 95% CI: 2.439, 27.331, P < 0.05), and peritumoral edema (HR: 3.748; 95% CI: 1.212, 11.594, P < 0.05) as independent predictors of OS. A nomogram integrating these predictors provided individualized risk assessment. This deep learning segmentation-based radiomics model demonstrated robust performance in predicting OS in GBM after maximal safe surgical resection. By incorporating radiomic signatures and advanced machine learning algorithms, it offers a non-invasive tool for personalized prognostic assessment and supports clinical decision-making.

Current trends and emerging themes in utilizing artificial intelligence to enhance anatomical diagnostic accuracy and efficiency in radiotherapy.

Pezzino S, Luca T, Castorina M, Puleo S, Castorina S

pubmed logopapersMay 19 2025
Artificial intelligence (AI) incorporation into healthcare has proven revolutionary, especially in radiotherapy, where accuracy is critical. The purpose of the study is to present patterns and develop topics in the application of AI to improve the precision of anatomical diagnosis, delineation of organs, and therapeutic effectiveness in radiation and radiological imaging. We performed a bibliometric analysis of scholarly articles in the fields starting in 2014. Through an examination of research output from key contributing nations and institutions, an analysis of notable research subjects, and an investigation of trends in scientific terminology pertaining to AI in radiology and radiotherapy. Furthermore, we examined software solutions based on AI in these domains, with a specific emphasis on extracting anatomical features and recognizing organs for the purpose of treatment planning. Our investigation found a significant surge in papers pertaining to AI in the fields since 2014. Institutions such as Emory University and Memorial Sloan-Kettering Cancer Center made substantial contributions to the development of the United States and China as leading research-producing nations. Key study areas encompassed adaptive radiation informed by anatomical alterations, MR-Linac for enhanced vision of soft tissues, and multi-organ segmentation for accurate planning of radiotherapy. An evident increase in the frequency of phrases such as 'radiomics,' 'radiotherapy segmentation,' and 'dosiomics' was noted. The evaluation of AI-based software revealed a wide range of uses in several subdisciplinary fields of radiation and radiology, particularly in improving the identification of anatomical features for treatment planning and identifying organs at risk. The incorporation of AI in anatomical diagnosis in radiological imaging and radiotherapy is progressing rapidly, with substantial capacity to transform the precision of diagnoses and the effectiveness of treatment planning.

New approaches to lesion assessment in multiple sclerosis.

Preziosa P, Filippi M, Rocca MA

pubmed logopapersMay 19 2025
To summarize recent advancements in artificial intelligence-driven lesion segmentation and novel neuroimaging modalities that enhance the identification and characterization of multiple sclerosis (MS) lesions, emphasizing their implications for clinical use and research. Artificial intelligence, particularly deep learning approaches, are revolutionizing MS lesion assessment and segmentation, improving accuracy, reproducibility, and efficiency. Artificial intelligence-based tools now enable automated detection not only of T2-hyperintense white matter lesions, but also of specific lesion subtypes, including gadolinium-enhancing, central vein sign-positive, paramagnetic rim, cortical, and spinal cord lesions, which hold diagnostic and prognostic value. Novel neuroimaging techniques such as quantitative susceptibility mapping (QSM), χ-separation imaging, and soma and neurite density imaging (SANDI), together with PET, are providing deeper insights into lesion pathology, better disentangling their heterogeneities and clinical relevance. Artificial intelligence-powered lesion segmentation tools hold great potential for improving fast, accurate and reproducible lesional assessment in the clinical scenario, thus improving MS diagnosis, monitoring, and treatment response assessment. Emerging neuroimaging modalities may contribute to advance the understanding MS pathophysiology, provide more specific markers of disease progression, and novel potential therapeutic targets.

Artificial intelligence based pulmonary vessel segmentation: an opportunity for automated three-dimensional planning of lung segmentectomy.

Mank QJ, Thabit A, Maat APWM, Siregar S, Van Walsum T, Kluin J, Sadeghi AH

pubmed logopapersMay 19 2025
This study aimed to develop an automated method for pulmonary artery and vein segmentation in both left and right lungs from computed tomography (CT) images using artificial intelligence (AI). The segmentations were evaluated using PulmoSR software, which provides 3D visualizations of patient-specific anatomy, potentially enhancing a surgeon's understanding of the lung structure. A dataset of 125 CT scans from lung segmentectomy patients at Erasmus MC was used. Manual annotations for pulmonary arteries and veins were created with 3D Slicer. nnU-Net models were trained for both lungs, assessed using Dice score, sensitivity, and specificity. Intraoperative recordings demonstrated clinical applicability. A paired t-test evaluated statistical significance of the differences between automatic and manual segmentations. The nnU-Net model, trained at full 3D resolution, achieved a mean Dice score between 0.91 and 0.92. The mean sensitivity and specificity were: left artery: 0.86 and 0.99, right artery: 0.84 and 0.99, left vein: 0.85 and 0.99, right vein: 0.85 and 0.99. The automatic method reduced segmentation time from ∼1.5 hours to under 5 min. Five cases were evaluated to demonstrate how the segmentations support lung segmentectomy procedures. P-values for Dice scores were all below 0.01, indicating statistical significance. The nnU-Net models successfully performed automatic segmentation of pulmonary arteries and veins in both lungs. When integrated with visualization tools, these automatic segmentations can enhance preoperative and intraoperative planning by providing detailed 3D views of patients anatomy.

Thymoma habitat segmentation and risk prediction model using CT imaging and K-means clustering.

Liang Z, Li J, He S, Li S, Cai R, Chen C, Zhang Y, Deng B, Wu Y

pubmed logopapersMay 19 2025
Thymomas, though rare, present a wide range of clinical behaviors, from indolent to aggressive forms, making accurate risk stratification crucial for treatment planning. Traditional methods such as histopathology and radiological assessments often lack the ability to capture tumor heterogeneity, which can impact prognosis. Radiomics, combined with machine learning, provides a method to extract and analyze quantitative imaging features, offering the potential to improve tumor classification and risk prediction. By segmenting tumors into distinct habitat zones, it becomes possible to assess intratumoral heterogeneity more effectively. This study employs radiomics and machine learning techniques to enhance thymoma risk prediction, aiming to improve diagnostic consistency and reduce variability in radiologists' assessments. This study aims to identify different habitat zones within thymomas through CT imaging feature analysis and to establish a predictive model to differentiate between high and low-risk thymomas. Additionally, the study explores how this model can assist radiologists. We obtained CT imaging data from 133 patients with thymoma who were treated at the Affiliated Hospital of Guangdong Medical University from 2015 to 2023. Images from the plain scan phase, venous phase, arterial phase, and their differential images (subtracted images) were used. Tumor regions were segmented into three habitat zones using K-Means clustering. Imaging features from each habitat zone were extracted using the PyRadiomics (van Griethuysen, 2017) library. The 28 most distinguishing features were selected through Mann-Whitney U tests (Mann, 1947) and Spearman's correlation analysis (Spearman, 1904). Five predictive models were built using the same machine learning algorithm (Support Vector Machine [SVM]): Habitat1, Habitat2, Habitat3 (trained on features from individual tumor habitat regions), Habitat All (trained on combined features from all regions), and Intra (trained on intratumoral features), and their performances were evaluated for comparison. The models' diagnostic outcomes were compared with the diagnoses of four radiologists (two junior and two experienced physicians). The AUC (area under curve) for habitat zone 1 was 0.818, for habitat zone 2 was 0.732, and for habitat zone 3 was 0.763. The comprehensive model, which combined data from all habitat zones, achieved an AUC of 0.960, outperforming the model based on traditional radiomic features (AUC of 0.720). The model significantly improved the diagnostic accuracy of all four radiologists. The AUCs for junior radiologists 1 and 2 increased from 0.747 and 0.775 to 0.932 and 0.972, respectively, while for experienced radiologists 1 and 2, the AUCs increased from 0.932 and 0.859 to 0.977 and 0.972, respectively. This study successfully identified distinct habitat zones within thymomas through CT imaging feature analysis and developed an efficient predictive model that significantly improved diagnostic accuracy. This model offers a novel tool for risk assessment of thymomas and can aid in guiding clinical decision-making.

Portable Ultrasound Bladder Volume Measurement Over Entire Volume Range Using a Deep Learning Artificial Intelligence Model in a Selected Cohort: A Proof of Principle Study.

Jeong HJ, Seol A, Lee S, Lim H, Lee M, Oh SJ

pubmed logopapersMay 19 2025
We aimed to prospectively investigate whether bladder volume measured using deep learning artificial intelligence (AI) algorithms (AI-BV) is more accurate than that measured using conventional methods (C-BV) if using a portable ultrasound bladder scanner (PUBS). Patients who underwent filling cystometry because of lower urinary tract symptoms between January 2021 and July 2022 were enrolled. Every time the bladder was filled serially with normal saline from 0 mL to maximum cystometric capacity in 50 mL increments, C-BV was measured using PUBS. Ultrasound images obtained during this process were manually annotated to define the bladder contour, which was used to build a deep learning AI model. The true bladder volume (T-BV) for each bladder volume range was compared with C-BV and AI-BV for analysis. We enrolled 250 patients (213 men and 37 women), and a deep learning AI model was established using 1912 bladder images. There was a significant difference between C-BV (205.5 ± 170.8 mL) and T-BV (190.5 ± 165.7 mL) (p = 0.001), but no significant difference between AI-BV (197.0 ± 161.1 mL) and T-BV (190.5 ± 165.7 mL) (p = 0.081). In bladder volume ranges of 101-150, 151-200, and 201-300 mL, there were significant differences in the percentage of volume differences between [C-BV and T-BV] and [AI-BV and T-BV] (p < 0.05), but no significant difference if converted to absolute values (p > 0.05). C-BV (R<sup>2</sup> = 0.91, p < 0.001) and AI-BV (R<sup>2</sup> = 0.90, p < 0.001) were highly correlated with T-BV. The mean difference between AI-BV and T-BV (6.5 ± 50.4) was significantly smaller than that between C-BV and T-BV (15.0 ± 50.9) (p = 0.001). Following image pre-processing, deep learning AI-BV more accurately estimated true BV than conventional methods in this selected cohort on internal validation. Determination of the clinical relevance of these findings and performance in external cohorts requires further study. The clinical trial was conducted using an approved product for its approved indication, so approval from the Ministry of Food and Drug Safety (MFDS) was not required. Therefore, there is no clinical trial registration number.

Federated Learning for Renal Tumor Segmentation and Classification on Multi-Center MRI Dataset.

Nguyen DT, Imami M, Zhao LM, Wu J, Borhani A, Mohseni A, Khunte M, Zhong Z, Shi V, Yao S, Wang Y, Loizou N, Silva AC, Zhang PJ, Zhang Z, Jiao Z, Kamel I, Liao WH, Bai H

pubmed logopapersMay 19 2025
Deep learning (DL) models for accurate renal tumor characterization may benefit from multi-center datasets for improved generalizability; however, data-sharing constraints necessitate privacy-preserving solutions like federated learning (FL). To assess the performance and reliability of FL for renal tumor segmentation and classification in multi-institutional MRI datasets. Retrospective multi-center study. A total of 987 patients (403 female) from six hospitals were included for analysis. 73% (723/987) had malignant renal tumors, primarily clear cell carcinoma (n = 509). Patients were split into training (n = 785), validation (n = 104), and test (n = 99) sets, stratified across three simulated institutions. MRI was performed at 1.5 T and 3 T using T2-weighted imaging (T2WI) and contrast-enhanced T1-weighted imaging (CE-T1WI) sequences. FL and non-FL approaches used nnU-Net for tumor segmentation and ResNet for its classification. FL-trained models across three simulated institutional clients with central weight aggregation, while the non-FL approach used centralized training on the full dataset. Segmentation was evaluated using Dice coefficients, and classification between malignant and benign lesions was assessed using accuracy, sensitivity, specificity, and area under the curves (AUCs). FL and non-FL performance was compared using the Wilcoxon test for segmentation Dice and Delong's test for AUC (p < 0.05). No significant difference was observed between FL and non-FL models in segmentation (Dice: 0.43 vs. 0.45, p = 0.202) or classification (AUC: 0.69 vs. 0.64, p = 0.959) on the test set. For classification, no significant difference was observed between the models in accuracy (p = 0.912), sensitivity (p = 0.862), or specificity (p = 0.847) on the test set. FL demonstrated comparable performance to non-FL approaches in renal tumor segmentation and classification, supporting its potential as a privacy-preserving alternative for multi-institutional DL models. 4. Stage 2.

Effect of low-dose colchicine on pericoronary inflammation and coronary plaque composition in chronic coronary disease: a subanalysis of the LoDoCo2 trial.

Fiolet ATL, Lin A, Kwiecinski J, Tutein Nolthenius J, McElhinney P, Grodecki K, Kietselaer B, Opstal TS, Cornel JH, Knol RJ, Schaap J, Aarts RAHM, Tutein Nolthenius AMFA, Nidorf SM, Velthuis BK, Dey D, Mosterd A

pubmed logopapersMay 19 2025
Low-dose colchicine (0.5 mg once daily) reduces the risk of major cardiovascular events in coronary disease, but its mechanism of action is not yet fully understood. We investigated whether low-dose colchicine is associated with changes in pericoronary inflammation and plaque composition in patients with chronic coronary disease. We performed a cross-sectional, nationwide, subanalysis of the Low-Dose Colchicine 2 Trial (LoDoCo2, n=5522). CT angiography studies were performed in 151 participants randomised to colchicine or placebo coronary after a median treatment duration of 28.2 months. Pericoronary adipose tissue (PCAT) attenuation measurements around proximal coronary artery segments and quantitative plaque analysis for the entire coronary tree were performed using artificial intelligence-enabled plaque analysis software. Median PCAT attenuation was not significantly different between the two groups (-79.5 Hounsfield units (HU) for colchicine versus -78.7 HU for placebo, p=0.236). Participants assigned to colchicine had a higher volume (169.6 mm<sup>3</sup> vs 113.1 mm<sup>3</sup>, p=0.041) and burden (9.6% vs 7.0%, p=0.035) of calcified plaque, and higher volume of dense calcified plaque (192.8 mm<sup>3</sup> vs 144.3 mm<sup>3</sup>, p=0.048) compared with placebo, independent of statin therapy. Colchicine treatment was associated with a lower burden of low-attenuation plaque in participants on a low-intensity statin, but not in those on a high-intensity statin (p<sub>interaction</sub>=0.037). Pericoronary inflammation did not differ among participants who received low-dose colchicine compared with placebo. Low-dose colchicine was associated with a higher volume of calcified plaque, particularly dense calcified plaque, which is considered a feature of plaque stability.
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