Understanding optic nerve structure and monitoring changes within it can provide insights into neurodegenerative diseases like multiple sclerosis, in which optic nerves are often damaged by inflammatory episodes of optic neuritis. Over the past decades, interest in the optic nerve has increased, particularly with advances in magnetic resonance technology and the advent of deep learning solutions. These advances have significantly improved the visualisation and analysis of optic nerves, making it possible to detect subtle changes that aid the early diagnosis and treatment of optic nerve-related diseases, and for planning radiotherapy interventions. Effective segmentation techniques, therefore, are crucial for enhancing the accuracy of predictive models, planning interventions and treatment strategies. This comprehensive review, which includes 27 peer-reviewed articles published between 2007 and 2024, examines and highlights the evolution of optic nerve magnetic resonance imaging segmentation over the past decade, tracing the development from intensity-based methods to the latest deep learning algorithms, including multi-atlas solutions using single or multiple image modalities.

Brain Tumor Segmentation (BraTS) plays a critical role in clinical diagnosis, treatment planning, and monitoring the progression of brain tumors. However, due to the variability in tumor appearance, size, and intensity across different MRI modalities, automated segmentation remains a challenging task. In this study, we propose a novel Transformer-based framework, multiPI-TransBTS, which integrates multi-physical information to enhance segmentation accuracy. The model leverages spatial information, semantic information, and multi-modal imaging data, addressing the inherent heterogeneity in brain tumor characteristics. The multiPI-TransBTS framework consists of an encoder, an Adaptive Feature Fusion (AFF) module, and a multi-source, multi-scale feature decoder. The encoder incorporates a multi-branch architecture to separately extract modality-specific features from different MRI sequences. The AFF module fuses information from multiple sources using channel-wise and element-wise attention, ensuring effective feature recalibration. The decoder combines both common and task-specific features through a Task-Specific Feature Introduction (TSFI) strategy, producing accurate segmentation outputs for Whole Tumor (WT), Tumor Core (TC), and Enhancing Tumor (ET) regions. Comprehensive evaluations on the BraTS2019 and BraTS2020 datasets demonstrate the superiority of multiPI-TransBTS over the state-of-the-art methods. The model consistently achieves better Dice coefficients, Hausdorff distances, and Sensitivity scores, highlighting its effectiveness in addressing the BraTS challenges. Our results also indicate the need for further exploration of the balance between precision and recall in the ET segmentation task. The proposed framework represents a significant advancement in BraTS, with potential implications for improving clinical outcomes for brain tumor patients.

Alzheimer's disease (AD) might impact the complexity of cerebral cortex, and the underlying biological mechanisms responsible for cortical changes in the AD cortex remain unclear. Fifty-eight participants with AD and 67 normal controls underwent high-resolution 3 T structural brain MRI. Using surface-based morphometry (SBM), we created vertex-wise maps for group comparisons in terms of five measures: cortical thickness, fractal dimension, gyrification index, Toro's gyrification index and sulcal depth respectively. Five machine learning (ML) models combining SBM parameters were established to predict AD. In addition, transcription-neuroimaging association analyses, as well as Mendelian randomization of AD and cortical thickness data, were conducted to investigate the genetic mechanisms and biological functions of AD. AD patients exhibited topological changes in cortical complexity, with increased complexity in the frontal and temporal cortex and decreased complexity in the insula cortex, alongside extensive cortical atrophy. Combining different SBM measures could aid disease diagnosis. The genes involved in cell structure support and the immune response were the strongest contributors to cortical anatomical features in AD patients. The identified genes associated with AD cortical morphology were overexpressed or underexpressed in excitatory neurons, oligodendrocytes, and astrocytes. Complexity alterations of the cerebral surface may be associated with a range of biological processes and molecular mechanisms, including immune responses. The present findings may contribute to a more comprehensive understanding of brain morphological patterns in AD patients.

Research in the cross-modal medical image translation domain has been very productive over the past few years in tackling the scarce availability of large curated multi-modality datasets with the promising performance of GAN-based architectures. However, only a few of these studies assessed task-based related performance of these synthetic data, especially for the training of deep models. We design and compare different GAN-based frameworks for generating synthetic brain[18F]fluorodeoxyglucose (FDG) PET images from T1 weighted MRI data. We first perform standard qualitative and quantitative visual quality evaluation. Then, we explore further impact of using these fake PET data in the training of a deep unsupervised anomaly detection (UAD) model designed to detect subtle epilepsy lesions in T1 MRI and FDG PET images. We introduce novel diagnostic task-oriented quality metrics of the synthetic FDG PET data tailored to our unsupervised detection task, then use these fake data to train a use case UAD model combining a deep representation learning based on siamese autoencoders with a OC-SVM density support estimation model. This model is trained on normal subjects only and allows the detection of any variation from the pattern of the normal population. We compare the detection performance of models trained on 35 paired real MR T1 of normal subjects paired either on 35 true PET images or on 35 synthetic PET images generated from the best performing generative models. Performance analysis is conducted on 17 exams of epilepsy patients undergoing surgery. The best performing GAN-based models allow generating realistic fake PET images of control subject with SSIM and PSNR values around 0.9 and 23.8, respectively and in distribution (ID) with regard to the true control dataset. The best UAD model trained on these synthetic normative PET data allows reaching 74% sensitivity. Our results confirm that GAN-based models are the best suited for MR T1 to FDG PET translation, outperforming transformer or diffusion models. We also demonstrate the diagnostic value of these synthetic data for the training of UAD models and evaluation on clinical exams of epilepsy patients. Our code and the normative image dataset are available.

Glioblastoma (GBM), primary central nervous system lymphoma (PCNSL), and brain metastases (BM) are common malignant brain tumors with similar radiological features, while the accurate and non-invasive dialgnosis is essential for selecting appropriate treatment plans. This study develops a deep learning model, FoTNet, to improve the automatic diagnosis accuracy of these tumors, particularly for the relatively rare PCNSL tumor. The model integrates a frequency-based channel attention layer and the focal loss to address the class imbalance issue caused by the limited samples of PCNSL. A multi-center MRI dataset was constructed by collecting and integrating data from Sir Run Run Shaw Hospital, along with public datasets from UPENN and TCGA. The dataset includes T1-weighted contrast-enhanced (T1-CE) MRI images from 58 GBM, 82 PCNSL, and 269 BM cases, which were divided into training and testing sets with a 5:2 ratio. FoTNet achieved a classification accuracy of 92.5 % and an average AUC of 0.9754 on the test set, significantly outperforming existing machine learning and deep learning methods in distinguishing among GBM, PCNSL, and BM. Through multiple validations, FoTNet has proven to be an effective and robust tool for accurately classifying these brain tumors, providing strong support for preoperative diagnosis and assisting clinicians in making more informed treatment decisions.

Transcranial photoacoustic computed tomography (PACT) holds significant potential as a neuroimaging modality. However, compensating for skull-induced aberrations in reconstructed images remains a challenge. Although optimization-based image reconstruction methods (OBRMs) can account for the relevant wave physics, they are computationally demanding and generally require accurate estimates of the skull's viscoelastic parameters. To circumvent these issues, a learning-based image reconstruction method was investigated for three-dimensional (3D) transcranial PACT. The method was systematically assessed in virtual imaging studies that involved stochastic 3D numerical head phantoms and applied to experimental data acquired by use of a physical head phantom that involved a human skull. The results demonstrated that the learning-based method yielded accurate images and exhibited robustness to errors in the assumed skull properties, while substantially reducing computational times compared to an OBRM. To the best of our knowledge, this is the first demonstration of a learned image reconstruction method for 3D transcranial PACT.

Focal cortical dysplasia (FCD) is a common cause of pharmacoresistant epilepsy. However, it can be challenging to detect FCD using MRI alone. This study aimed to review and analyze studies that used machine learning and artificial neural networks (ANN) methods as an additional tool to enhance MRI findings in FCD patients. A systematic search was conducted in four databases (Embase, PubMed, Scopus, and Web of Science). The quality of the studies was assessed using QUADAS-AI, and a bivariate random-effects model was used for analysis. The main outcome analyzed was the sensitivity and specificity of patient-wise outcomes. Heterogeneity among studies was assessed using I². A total of 41 studies met the inclusion criteria, including 24 ANN-based studies and 17 machine learning studies. Meta-analysis of internal validation datasets showed a pooled sensitivity of 0.81 and specificity of 0.92 for AI-based models in detecting FCD lesions. Meta-analysis of external validation datasets yielded a pooled sensitivity of 0.73 and specificity of 0.66. There was moderate heterogeneity among studies in the external validation dataset, but no significant publication bias was found. Although there is an increasing number of machine learning and ANN-based models for FCD detection, their clinical applicability remains limited. Further refinement and optimization, along with longitudinal studies, are needed to ensure their integration into clinical practice. Addressing the identified limitations and intensifying research efforts will improve their relevance and reliability in real medical scenarios.

Global aging raises concerns about cognitive health, metabolic disorders, and sarcopenia. Prevention of reversible decline and diseases in middle-aged individuals is essential for promoting healthy aging. We hypothesize that changes in body composition, specifically muscle mass and visceral fat, and metabolic indices are associated with accelerated brain aging. To explore these relationships, we employed a brain age model to investigate the links between the brain age gap (BAG), body composition, and metabolic markers. Using T1-weighted anatomical brain MRIs, we developed a machine learning model to predict brain age from gray matter features, trained on 2,675 healthy individuals aged 18-92 years. This model was then applied to a separate cohort of 458 Taiwanese adults (57.8 years ± 11.6; 280 men) to assess associations between BAG, body composition quantified by MRI, and metabolic markers. Our model demonstrated reliable generalizability for predicting individual age in the clinical dataset (MAE = 6.11 years, r = 0.900). Key findings included significant correlations between larger BAG and reduced total abdominal muscle area (r = -0.146, p = 0.018), lower BMI-adjusted skeletal muscle indices, (r = -0.134, p = 0.030), increased systemic inflammation, as indicated by high-sensitivity C-reactive protein levels (r = 0.121, p = 0.048), and elevated fasting glucose levels (r = 0.149, p = 0.020). Our findings confirm that muscle mass and metabolic health decline are associated with accelerated brain aging. Interventions to improve muscle health and metabolic control may mitigate adverse effects of brain aging, supporting healthier aging trajectories.

This paper presents MSLesSeg, a new, publicly accessible MRI dataset designed to advance research in Multiple Sclerosis (MS) lesion segmentation. The dataset comprises 115 scans of 75 patients including T1, T2 and FLAIR sequences, along with supplementary clinical data collected across different sources. Expert-validated annotations provide high-quality lesion segmentation labels, establishing a reliable human-labeled dataset for benchmarking. Part of the dataset was shared with expert scientists with the aim to compare the last automatic AI-based image segmentation solutions with an expert-biased handmade segmentation. In addition, an AI-based lesion segmentation of MSLesSeg was developed and technically validated against the last state-of-the-art methods. The dataset, the detailed analysis of researcher contributions, and the baseline results presented here mark a significant milestone for advancing automated MS lesion segmentation research.

Magnetic resonance imaging (MRI), combined with artificial intelligence techniques, has improved our understanding of brain structural change and enabled the estimation of brain age. Neurodegenerative disorders, such as Alzheimer's disease (AD), have been linked to accelerated brain aging. In this study, we aimed to develop a deep-learning framework that processes and integrates MRI images to more accurately predict brain age, cognitive function, and amyloid pathology. In this study, we aimed to develop a deep-learning framework that processes and integrates MRI images to more accurately predict brain age, cognitive function, and amyloid pathology.We collected over 10,000 T1-weighted MRI scans from more than 7,000 individuals across six cohorts. We designed a multi-modal deep-learning framework that employs 3D convolutional neural networks to analyze MRI and additional neural networks to evaluate demographic data. Our initial model focused on predicting brain age, serving as a foundational model from which we developed separate models for cognition function and amyloid plaque prediction through transfer learning. The brain age prediction model achieved the mean absolute error (MAE) for cognitive normal population in the ADNI (test) datasets of 3.302 years. The gap between predicted brain age and chronological age significantly increases while cognition declines. The cognition prediction model exhibited a root mean square error (RMSE) of 0.334 for the Clinical Dementia Rating (CDR) regression task, achieving an area under the curve (AUC) of approximately 0.95 in identifying ing dementia patients. Dementia related brain regions, such as the medial temporal lobe, were identified by our model. Finally, amyloid plaque prediction model was trained to predict amyloid plaque, and achieved an AUC about 0.8 for dementia patients. These findings indicate that the present predictive models can identify subtle changes in brain structure, enabling precise estimates of brain age, cognitive status, and amyloid pathology. Such models could facilitate the use of MRI as a non-invasive diagnostic tool for neurodegenerative diseases, including AD.