Accurate compensation of brain deformation is critical for reliable image-guided neurosurgery. Surgical manipulation and tumor resection induce tissue motion, causing preoperative planning images to become misaligned with the intraoperative anatomy. In this review, we examine data-driven methods developed between 2020 and 2025 for brain deformation registration and modeling, with a particular focus on learning-based approaches. A comprehensive literature search was conducted in PubMed, IEEE Xplore, Scopus, and Web of Science using predefined inclusion and exclusion criteria for computational methods addressing brain deformation in neurosurgical imaging, resulting in 46 eligible studies. We provide a unified analysis of methodological strategies, including deep learning-based image registration, direct deformation field regression, synthesis-driven multimodal alignment, resection-aware architectures for handling missing correspondences, and hybrid models integrating biomechanical priors. We also examine dataset utilization, evaluation metrics, validation protocols, and the assessment of uncertainty and generalization across studies. While learning-based methods demonstrate promising accuracy and computational efficiency, current approaches remain limited by out-of-distribution robustness, standardized benchmarking, interpretability, and readiness for clinical deployment. Our review highlights these gaps and outlines future directions toward more robust, generalizable, and clinically translatable solutions for neurosurgical guidance. By organizing recent advances and critically assessing evaluation practices, this work provides a comprehensive reference for researchers and clinicians working on data-driven registration and modeling of brain deformation.

Hypoxic Ischemic Encephalopathy (HIE) represents a brain dysfunction, affecting approximately 1 to 5 per 1000 full-term neonates. The precise delineation and segmentation of HIE-related lesions in neonatal brain Magnetic Resonance Images (MRI) are pivotal in advancing outcome predictions, identifying patients at high risk, elucidating neurological manifestations, and assessing treatment efficacies. Despite its importance, the development of algorithms for segmenting HIE lesions from MRI volumes has been impeded by data scarcity. Addressing this critical gap, we organized the first BONBID-HIE challenge with diffusion MRI data (Apparent Diffusion Coefficient (ADC) maps) for HIE lesion segmentation, in conjunction with the MICCAI 2023. Totally 14 algorithms were submitted, employing a gamut of cutting-edge automatic machine-learning-based segmentation algorithms. Our comprehensive analysis of HIE lesion segmentation and submitted algorithms facilitates an in-depth evaluation of the current technological zenith, outlines directions for future advancements, and highlights persistent hurdles. To foster ongoing research and benchmarking, the annotated HIE dataset, developed algorithm dockers, and unified evaluation codes are accessible through a dedicated online platform (https://bonbid-hie2023.grand-challenge.org).

Medical Visual Question Answering (MVQA) requires AI models to answer questions related to medical images, offering significant potential to assist medical professionals in evaluating and diagnosing diseases, thereby improving early interventions. However, existing MVQA datasets primarily focus on basic questions regarding visual perception and pattern recognition, without addressing the more complex questions that are critical in clinical diagnosis and decision-making. This paper introduces a new benchmark designed for professional-level medical reasoning, simulating the decision-making process. We achieve this by collecting MRI and clinical data related to Hypoxic-Ischemic Encephalopathy, enriched with expert annotations and insights. Building on this data, we generate clinical question-answer pairs and MRI interpretations to enable comprehensive diagnosis, interpretation, and prediction of neurocognitive outcomes. Our evaluation of current large vision-language models (LVLMs) shows limited performance on this benchmark, highlighting both the challenges of the task and the importance of this benchmark for advancing medical AI. Furthermore, we propose a novel ``Clinical Graph of Thoughts" model, which integrates domain-specific medical knowledge and clinical reasoning processes with the interpretive abilities of LVLMs. The model demonstrates promising results, achieving around 15\% absolute gain on the most important neurocognitive outcome task, while the benchmark still reveals substantial opportunities for further research innovation.

Most deep learning models for temporal regression directly output the estimation based on single input images, ignoring the relationships between different images. In this paper, we propose deep relation learning for regression, aiming to learn different relations between a pair of input images. Four non-linear relations are considered: "cumulative relation," "relative relation," "maximal relation" and "minimal relation." These four relations are learned simultaneously from one deep neural network which has two parts: feature extraction and relation regression. We use an efficient convolutional neural network to extract deep features from the pair of input images and apply a Transformer for relation learning. The proposed method is evaluated on a merged dataset with 6,049 subjects with ages of 0-97 years using 5-fold cross-validation for the task of brain age estimation. The experimental results have shown that the proposed method achieved a mean absolute error (MAE) of 2.38 years, which is lower than the MAEs of 8 other state-of-the-art algorithms with statistical significance (p<0.05) in paired T-test (two-side).

Deep learning can provide rapid brain age estimation based on brain magnetic resonance imaging (MRI). However, most studies use one neural network to extract the global information from the whole input image, ignoring the local fine-grained details. In this paper, we propose a global-local transformer, which consists of a global-pathway to extract the global-context information from the whole input image and a local-pathway to extract the local fine-grained details from local patches. The fine-grained information from the local patches are fused with the global-context information by the attention mechanism, inspired by the transformer, to estimate the brain age. We evaluate the proposed method on 8 public datasets with 8,379 healthy brain MRIs with the age range of 0-97 years. 6 datasets are used for cross-validation and 2 datasets are used for evaluating the generality. Comparing with other state-of-the-art methods, the proposed global-local transformer reduces the mean absolute error of the estimated ages to 2.70 years and increases the correlation coefficient of the estimated age and the chronological age to 0.9853. In addition, our proposed method provides regional information of which local patches are most informative for brain age estimation. Our source code is available on: https://github.com/shengfly/global-local-transformer.

In brain tumor surgery, the quality and safety of the procedure can be impacted by intra-operative tissue deformation, called brain shift. Brain shift can move the surgical targets and other vital structures such as blood vessels, thus invalidating the pre-surgical plan. Intra-operative ultrasound (iUS) is a convenient and cost-effective imaging tool to track brain shift and tumor resection. Accurate image registration techniques that update pre-surgical MRI based on iUS are crucial but challenging. The MICCAI Challenge 2018 for Correction of Brain shift with Intra-Operative UltraSound (CuRIOUS2018) provided a public platform to benchmark MRI-iUS registration algorithms on newly released clinical datasets. In this work, we present the data, setup, evaluation, and results of CuRIOUS 2018, which received 6 fully automated algorithms from leading academic and industrial research groups. All algorithms were first trained with the public RESECT database, and then ranked based on a test dataset of 10 additional cases with identical data curation and annotation protocols as the RESECT database. The article compares the results of all participating teams and discusses the insights gained from the challenge, as well as future work.

Evaluating various algorithms for the inter-subject registration of brain magnetic resonance images (MRI) is a necessary topic receiving growing attention. Existing studies evaluated image registration algorithms in specific tasks or using specific databases (e.g., only for skull-stripped images, only for single-site images, etc.). Consequently, the choice of registration algorithms seems task- and usage/parameter-dependent. Nevertheless, recent large-scale, often multi-institutional imaging-related studies create the need and raise the question whether some registration algorithms can 1) generally apply to various tasks/databases posing various challenges; 2) perform consistently well, and while doing so, 3) require minimal or ideally no parameter tuning. In seeking answers to this question, we evaluated 12 general-purpose registration algorithms, for their generality, accuracy and robustness. We fixed their parameters at values suggested by algorithm developers as reported in the literature. We tested them in 7 databases/tasks, which present one or more of 4 commonly-encountered challenges: 1) inter-subject anatomical variability in skull-stripped images; 2) intensity homogeneity, noise and large structural differences in raw images; 3) imaging protocol and field-of-view (FOV) differences in multi-site data; and 4) missing correspondences in pathology-bearing images. Totally 7,562 registrations were performed. Registration accuracies were measured by (multi-)expert-annotated landmarks or regions of interest (ROIs). To ensure reproducibility, we used public software tools, public databases (whenever possible), and we fully disclose the parameter settings. We show evaluation results, and discuss the performances in light of algorithms' similarity metrics, transformation models and optimization strategies. We also discuss future directions for the algorithm development and evaluations.