# Brain Imaging Foundation Models, Are We There Yet? A Systematic Review of Foundation Models for Brain Imaging and Biomedical Research

arXiv: https://arxiv.org/abs/2506.13306 · HTML: https://mlsanity.com/paper/2506.13306/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 68 of its 164 references that are in the map.
- First posted on arXiv 16 Jun 2025.

## Builds on (most cited first, 30 of 68)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [GShard: Scaling Giant Models with Conditional Computation and Automatic Sharding](https://mlsanity.com/paper/2006.16668/) (2020)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [Med-Flamingo: a Multimodal Medical Few-shot Learner](https://mlsanity.com/paper/2307.15189/) (2023)
- [PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering](https://mlsanity.com/paper/2305.10415/) (2023)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [AnomalyCLIP: Object-agnostic Prompt Learning for Zero-shot Anomaly Detection](https://mlsanity.com/paper/2310.18961/) (2023)
- [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](https://mlsanity.com/paper/2303.07240/) (2023)
- [BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2305.17100/) (2023)
- [A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics](https://mlsanity.com/paper/2310.05694/) (2023)
- [Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis](https://mlsanity.com/paper/1908.06912/) (2019)
- [Medical SAM 2: Segment medical images as video via Segment Anything Model 2](https://mlsanity.com/paper/2408.00874/) (2024)
- [On the Challenges and Perspectives of Foundation Models for Medical Image Analysis](https://mlsanity.com/paper/2306.05705/) (2023)
- [MedSegDiff-V2: Diffusion based Medical Image Segmentation with Transformer](https://mlsanity.com/paper/2301.11798/) (2023)
- [A Survey of Large Language Models in Medicine: Progress, Application, and Challenge](https://mlsanity.com/paper/2311.05112/) (2023)
- [Heterogeneous LoRA for Federated Fine-tuning of On-Device Foundation Models](https://mlsanity.com/paper/2401.06432/) (2024)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [Multi-Modal Masked Autoencoders for Medical Vision-and-Language Pre-Training](https://mlsanity.com/paper/2209.07098/) (2022)
- [STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training](https://mlsanity.com/paper/2304.06716/) (2023)
- [Segment Anything Model for Medical Image Segmentation: Current Applications and Future Directions](https://mlsanity.com/paper/2401.03495/) (2024)
- [Sparse Low-rank Adaptation of Pre-trained Language Models](https://mlsanity.com/paper/2311.11696/) (2023)
- [Pre-trained Language Models in Biomedical Domain: A Systematic Survey](https://mlsanity.com/paper/2110.05006/) (2021)
- [SegVol: Universal and Interactive Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2311.13385/) (2023)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)

## Abstract (arXiv)

Foundation models (FMs), large neural networks pretrained on extensive and diverse datasets, have revolutionized artificial intelligence and shown significant promise in medical imaging by enabling robust performance with limited labeled data. Although numerous surveys have reviewed the application of FM in healthcare care, brain imaging remains underrepresented, despite its critical role in the diagnosis and treatment of neurological diseases using modalities such as MRI, CT, and PET. Existing reviews either marginalize brain imaging or lack depth on the unique challenges and requirements of FM in this domain, such as multimodal data integration, support for diverse clinical tasks, and handling of heterogeneous, fragmented datasets. To address this gap, we present the first comprehensive and curated review of FMs for brain imaging. We systematically analyze 161 brain imaging datasets and 86 FM architectures, providing information on key design choices, training paradigms, and optimizations driving recent advances. Our review highlights the leading models for various brain imaging tasks, summarizes their innovations, and critically examines current limitations and blind spots in the literature. We conclude by outlining future research directions to advance FM applications in brain imaging, with the aim of fostering progress in both clinical and research settings.