Automated thalamic nuclear segmentation has contributed towards a shift in neuroimaging analyses from treating the thalamus as a homogeneous, passive relay, to a set of individual nuclei, embedded within distinct brain-wide circuits. However, many studies continue to widely rely on FreeSurfers segmentation of T1-weighted structural MRIs, despite their poor intrathalamic nuclear contrast. Meanwhile, a convolutional neural network tool has been developed for FreeSurfer, using information from both diffusion and T1-weighted MRIs. Another popular thalamic nuclear segmentation technique is HIPS-THOMAS, a multi-atlas-based method that leverages white-matter-like contrast synthesized from T1-weighted MRIs. However, rigorous comparisons amongst methods remain scant, and the thalamic atlases against which these methods have been assessed have their own limitations. These issues may compromise the quality of cross-species comparisons, structural and functional connectivity studies in health and disease, as well as the efficacy of neuromodulatory interventions targeting the thalamus. Here, we report, for the first time, comparisons amongst HIPS-THOMAS, the standard FreeSurfer segmentation, and its more recent development, against two thalamic atlases as silver-standard ground-truths. We used two cohorts of healthy adults, and one cohort of patients in the chronic phase of autoimmune limbic encephalitis. In healthy adults, HIPS-THOMAS surpassed, not only the standard FreeSurfer segmentation, but also its more recent, diffusion-based update. The improvements made with the latter relative to the former were limited to a few nuclei. Finally, the standard FreeSurfer method underperformed, relative to the other two, in distinguishing between patients and healthy controls based on the affected anteroventral and pulvinar nuclei. In light of the above findings, we provide recommendations on the use of automated segmentation methods of the human thalamus using structural brain imaging.

The volume of in vivo human brains is determined with various MRI measurement tools that have not been assessed against a gold standard. The purpose of this study was to validate the MRI brain volumes by scanning ex vivo, in situ specimens, which allows the extraction of the brain after the scan to compare its volume with the gold-standard water displacement method (WDM). The 3T MRI T₂-weighted, T₁-weighted, and MP2RAGE images of seven anatomical heads fixed with an alcohol-formaldehyde solution were acquired. The gray and white matter were assessed using two methods: (i) a manual intensity-based threshold segmentation using Display (MINC-ToolKit) and (ii) an automatic deep learning-based segmentation tool (SynthSeg). The brains were extracted and their volumes measured with the WDM after the removal of their meninges and a midsagittal cut. Volumes from all methods were compared with the ground truth (WDM volumes) using a repeated-measures analysis of variance. Mean brain volumes, in cubic centimeters, were 1111.14 ± 121.78 for WDM, 1020.29 ± 70.01 for manual T₂-weighted, 1056.29 ± 90.54 for automatic T₂-weighted, 1094.69 ± 100.51 for automatic T₁-weighted, 1066.56 ± 96.52 for automatic magnetization-prepared 2 rapid gradient-echo first inversion time, and 1156.18 ± 121.87 for automatic magnetization-prepared 2 rapid gradient-echo second inversion time. All volumetry methods were significantly different (F = 17.874; p < 0.001) from the WDM volumes, except the automatic T₁-weighted volumes. SynthSeg accurately determined the brain volume in ex vivo, in situ T₁-weighted MRI scans. The results suggested that given the contrast similarity between the ex vivo and in vivo sequences, the brain volumes of clinical studies are most probably sufficiently accurate, with some degree of underestimation depending on the sequence used.

Cerebrovascular imaging has undergone significant advances, enhancing the diagnosis and management of cerebrovascular diseases such as stroke, aneurysms, and arteriovenous malformations. This chapter explores key imaging modalities, including non-contrast computed tomography, computed tomography angiography, magnetic resonance imaging (MRI), and digital subtraction angiography. Innovations such as high-resolution vessel wall imaging, artificial intelligence (AI)-driven stroke detection, and advanced perfusion imaging have improved diagnostic accuracy and treatment selection. Additionally, novel techniques like 7-T MRI, molecular imaging, and functional ultrasound provide deeper insights into vascular pathology. AI and machine learning applications are revolutionizing automated detection and prognostication, expediting treatment decisions. Challenges remain in standardization, radiation exposure, and accessibility. However, continued technological advances, multimodal imaging integration, and AI-driven automation promise a future of precise, non-invasive cerebrovascular diagnostics, ultimately improving patient outcomes.

Alzheimer's disease (AD) poses a significant global health challenge, necessitating early and accurate diagnosis to enable timely intervention. Structural MRI (sMRI) is a key imaging modality for detecting AD-related brain atrophy, yet traditional deep learning models like convolutional neural networks (CNNs) struggle to capture complex spatial dependencies critical for AD diagnosis. This study introduces the Regional Attention-Enhanced Vision Transformer (RAE-ViT), a novel framework designed for AD classification using sMRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. RAE-ViT leverages regional attention mechanisms to prioritize disease-critical brain regions, such as the hippocampus and ventricles, while integrating hierarchical self-attention and multi-scale feature extraction to model both localized and global structural patterns. Evaluated on 1152 sMRI scans (255 AD, 521 MCI, 376 NC), RAE-ViT achieved state-of-the-art performance with 94.2 % accuracy, 91.8 % sensitivity, 95.7 % specificity, and an AUC of 0.96, surpassing standard ViTs (89.5 %) and CNN-based models (e.g., ResNet-50: 87.8 %). The model's interpretable attention maps align closely with clinical biomarkers (Dice: 0.89 hippocampus, 0.85 ventricles), enhancing diagnostic reliability. Robustness to scanner variability (92.5 % accuracy on 1.5T scans) and noise (92.5 % accuracy under 10 % Gaussian noise) further supports its clinical applicability. A preliminary multimodal extension integrating sMRI and PET data improved accuracy to 95.8 %. Future work will focus on optimizing RAE-ViT for edge devices, incorporating multimodal data (e.g., PET, fMRI, genetic), and exploring self-supervised and federated learning to enhance generalizability and privacy. RAE-ViT represents a significant advancement in AI-driven AD diagnosis, offering potential for early detection and improved patient outcomes.

Large Language Models (LLMs) have shown strong performance in text-based healthcare tasks. However, their utility in image-based applications remains unexplored. We investigate the effectiveness of LLMs for medical imaging tasks, specifically glioma classification and segmentation, and compare their performance to that of traditional convolutional neural networks (CNNs). Using the BraTS 2020 dataset of multi-modal brain MRIs, we evaluated a general-purpose vision-language LLM (LLaMA 3.2 Instruct) both before and after fine-tuning, and benchmarked its performance against custom 3D CNNs. For glioma classification (Low-Grade vs. High-Grade), the CNN achieved 80% accuracy and balanced precision and recall. The general LLM reached 76% accuracy but suffered from a specificity of only 18%, often misclassifying Low-Grade tumors. Fine-tuning improved specificity to 55%, but overall performance declined (e.g., accuracy dropped to 72%). For segmentation, three methods - center point, bounding box, and polygon extraction, were implemented. CNNs accurately localized gliomas, though small tumors were sometimes missed. In contrast, LLMs consistently clustered predictions near the image center, with no distinction of glioma size, location, or placement. Fine-tuning improved output formatting but failed to meaningfully enhance spatial accuracy. The bounding polygon method yielded random, unstructured outputs. Overall, CNNs outperformed LLMs in both tasks. LLMs showed limited spatial understanding and minimal improvement from fine-tuning, indicating that, in their current form, they are not well-suited for image-based tasks. More rigorous fine-tuning or alternative training strategies may be needed for LLMs to achieve better performance, robustness, and utility in the medical space.

Brain tumour detection and classification are critical for improving patient prognosis and treatment planning. However, manual identification from magnetic resonance imaging (MRI) scans is time-consuming, error-prone, and reliant on expert interpretation. The increasing complexity of tumour characteristics necessitates automated solutions to enhance accuracy and efficiency. This study introduces a novel ensemble deep learning model, boosted deformable and residual convolutional network with bi-directional convolutional long short-term memory (BDefRCNLSTM), for the classification and segmentation of brain tumours. The proposed framework integrates entropy-based local binary pattern (ELBP) for extracting spatial semantic features and employs the enhanced sooty tern optimisation (ESTO) algorithm for optimal feature selection. Additionally, an improved X-Net model is utilised for precise segmentation of tumour regions. The model is trained and evaluated on Figshare, Brain MRI, and Kaggle datasets using multiple performance metrics. Experimental results demonstrate that the proposed BDefRCNLSTM model achieves over 99% accuracy in both classification and segmentation, outperforming existing state-of-the-art approaches. The findings establish the proposed approach as a clinically viable solution for automated brain tumour diagnosis. The integration of optimised feature selection and advanced segmentation techniques improves diagnostic accuracy, potentially assisting radiologists in making faster and more reliable decisions.

Robust 3D brain tumor MRI segmentation is significant for diagnosis and treatment. However, the tumor heterogeneity, irregular shape, and complicated texture are challenging. Deep learning has transformed medical image analysis by feature extraction directly from the data, greatly enhancing the accuracy of segmentation. The functionality of deep models can be complemented by adding modules like texture-sensitive customized convolution layers and attention mechanisms. These components allow the model to focus its attention on pertinent locations and boundary definition problems. In this paper, a texture-aware deep learning method that improves the U-Net structure by adding a trainable Gabor convolution layer in the input for rich textural feature capture is proposed. Such features are fused in parallel with standard convolutional outputs to better represent tumors. The model also utilizes dual attention modules, Squeeze-and-Excitation blocks in the encoder for dynamically adjusting channel-wise features and Attention Gates for boosting skip connections by removing trivial areas and weighting tumor areas. The working of each module is explored through explainable artificial intelligence methods to ensure interpretability. To address class imbalance, a weighted combined loss function is applied. The model achieves Dice coefficients of 91.62%, 89.92%, and 88.86% for whole tumor, tumor core, and enhancing tumor respectively on BraTS2021 dataset. Large-scale quantitative and qualitative evaluations on BraTS2021, validated on BraTS benchmarks, prove the accuracy and robustness of the proposed model. The proposed approach results are superior to benchmark U-Net and other state-of-the-art segmentation methods, offering a robust and interpretable solution for clinical use.

Intraoperative tumor imaging is critical to achieving maximal safe resection during neurosurgery, especially for low-grade glioma resection. Given the convenience of ultrasound as an intraoperative imaging modality, but also the limitations of the ultrasound modality and the time-consuming process of manual tumor segmentation, we propose a learning-based model for the accurate segmentation of low-grade gliomas in ultrasound images. We developed a novel U-net-based architecture adopting the block architecture of the ConvNext V2 model, titled U-ConvNext, which also incorporates various architectural improvements including global response normalization, fine-tuned kernel sizes, and inception layers. We also adopted the CutMix data augmentation technique for semantic segmentation, aiming for enhanced texture detection. Conformal segmentation, a novel approach to conformal prediction for binary semantic segmentation, was also developed for uncertainty quantification, providing calibrated measures of model uncertainty in a visual format. The proposed models were trained and evaluated on three subsets of images in the RESECT dataset and achieved hold-out test Dice scores of 84.63%, 74.52%, and 90.82% on the "before," "during," and "after" subsets, respectively, which indicates increases of ~ 13-31% compared to the state of the art. Furthermore, external evaluation on the ReMIND dataset indicated a robust performance (dice score of 79.17% [95% CI: 77.82-81.62] and only a moderate decline of < 3% in expected calibration error. Our approach integrates various innovations in model design, model training, and uncertainty quantification, achieving improved results on the segmentation of low-grade glioma in ultrasound images during neurosurgery.

Gliomas are the most prevalent type of primary brain tumors, and their accurate segmentation from MRI is critical for diagnosis, treatment planning, and longitudinal monitoring. However, the scarcity of high-quality annotated imaging data in Sub-Saharan Africa (SSA) poses a significant challenge for deploying advanced segmentation models in clinical workflows. This study introduces a robust and computationally efficient deep learning framework tailored for resource-constrained settings. We leveraged a 3D Attention UNet architecture augmented with residual blocks and enhanced through transfer learning from pre-trained weights on the BraTS 2021 dataset. Our model was evaluated on 95 MRI cases from the BraTS-Africa dataset, a benchmark for glioma segmentation in SSA MRI data. Despite the limited data quality and quantity, our approach achieved Dice scores of 0.76 for the Enhancing Tumor (ET), 0.80 for Necrotic and Non-Enhancing Tumor Core (NETC), and 0.85 for Surrounding Non-Functional Hemisphere (SNFH). These results demonstrate the generalizability of the proposed model and its potential to support clinical decision making in low-resource settings. The compact architecture, approximately 90 MB, and sub-minute per-volume inference time on consumer-grade hardware further underscore its practicality for deployment in SSA health systems. This work contributes toward closing the gap in equitable AI for global health by empowering underserved regions with high-performing and accessible medical imaging solutions.

Magnetic resonance imaging (MRI) is the gold standard for brain imaging. Deep learning (DL) algorithms have been proposed to aid in the diagnosis of diseases such as Alzheimer's disease (AD) from MRI scans. However, DL algorithms can suffer from shortcut learning, in which spurious features, not directly related to the output label, are used for prediction. When these features are related to protected attributes, they can lead to performance bias against underrepresented protected groups, such as those defined by race and sex. In this work, we explore the potential for shortcut learning and demographic bias in DL based AD diagnosis from MRI. We first investigate if DL algorithms can identify race or sex from 3D brain MRI scans to establish the presence or otherwise of race and sex based distributional shifts. Next, we investigate whether training set imbalance by race or sex can cause a drop in model performance, indicating shortcut learning and bias. Finally, we conduct a quantitative and qualitative analysis of feature attributions in different brain regions for both the protected attribute and AD classification tasks. Through these experiments, and using multiple datasets and DL models (ResNet and SwinTransformer), we demonstrate the existence of both race and sex based shortcut learning and bias in DL based AD classification. Our work lays the foundation for fairer DL diagnostic tools in brain MRI. The code is provided at https://github.com/acharaakshit/ShortMR