Brain imaging analysis is fundamental in neuroscience, providing valuable insights into brain structure and function. Traditional workflows follow a sequential pipeline--brain extraction, registration, segmentation, parcellation, network generation, and classification--treating each step as an independent task. These methods rely heavily on task-specific training data and expert intervention to correct intermediate errors, making them particularly burdensome for high-dimensional neuroimaging data, where annotations and quality control are costly and time-consuming. We introduce Uni-Brain, a unified end-to-end framework that integrates all processing steps into a single optimization process, allowing tasks to interact and refine each other. Unlike traditional approaches that require extensive task-specific annotations, UniBrain operates with minimal supervision, leveraging only low-cost labels ( i.e., classification and extraction) and a single labeled atlas. By jointly optimizing extraction, registration, segmentation, parcellation, network generation, and classification, UniBrain enhances both accuracy and computational efficiency while significantly reducing annotation effort. Experimental results demonstrate its superiority over existing methods across multiple tasks, offering a more scalable and reliable solution for neuroimaging analysis.

Magnetic resonance imaging~(MRI) have played a crucial role in brain disease diagnosis, with which a range of computer-aided artificial intelligence methods have been proposed. However, the early explorations usually focus on the limited types of brain diseases in one study and train the model on the data in a small scale, yielding the bottleneck of generalization. Towards a more effective and scalable paradigm, we propose a hierarchical knowledge-enhanced pre-training framework for the universal brain MRI diagnosis, termed as UniBrain. Specifically, UniBrain leverages a large-scale dataset of 24,770 imaging-report pairs from routine diagnostics. Different from previous pre-training techniques for the unitary vision or textual feature, or with the brute-force alignment between vision and language information, we leverage the unique characteristic of report information in different granularity to build a hierarchical alignment mechanism, which strengthens the efficiency in feature learning. Our UniBrain is validated on three real world datasets with severe class imbalance and the public BraTS2019 dataset. It not only consistently outperforms all state-of-the-art diagnostic methods by a large margin and provides a superior grounding performance but also shows comparable performance compared to expert radiologists on certain disease types.

Image reconstruction and captioning from brain activity evoked by visual stimuli allow researchers to further understand the connection between the human brain and the visual perception system. While deep generative models have recently been employed in this field, reconstructing realistic captions and images with both low-level details and high semantic fidelity is still a challenging problem. In this work, we propose UniBrain: Unify Image Reconstruction and Captioning All in One Diffusion Model from Human Brain Activity. For the first time, we unify image reconstruction and captioning from visual-evoked functional magnetic resonance imaging (fMRI) through a latent diffusion model termed Versatile Diffusion. Specifically, we transform fMRI voxels into text and image latent for low-level information and guide the backward diffusion process through fMRI-based image and text conditions derived from CLIP to generate realistic captions and images. UniBrain outperforms current methods both qualitatively and quantitatively in terms of image reconstruction and reports image captioning results for the first time on the Natural Scenes Dataset (NSD) dataset. Moreover, the ablation experiments and functional region-of-interest (ROI) analysis further exhibit the superiority of UniBrain and provide comprehensive insight for visual-evoked brain decoding.