# Deep generative priors for 3D brain analysis

arXiv: https://arxiv.org/abs/2510.15119 · HTML: https://mlsanity.com/paper/2510.15119/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 36 of its 63 references that are in the map.
- First posted on arXiv 16 Oct 2025.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 30 of 36)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [The Unreasonable Effectiveness of Deep Features as a Perceptual Metric](https://mlsanity.com/paper/1801.03924/) (2018)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [Denoising Diffusion Restoration Models](https://mlsanity.com/paper/2201.11793/) (2022)
- [Zero-Shot Image Restoration Using Denoising Diffusion Null-Space Model](https://mlsanity.com/paper/2212.00490/) (2022)
- [Solving Inverse Problems in Medical Imaging with Score-Based Generative Models](https://mlsanity.com/paper/2111.08005/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Improving Diffusion Models for Inverse Problems using Manifold Constraints](https://mlsanity.com/paper/2206.00941/) (2022)
- [Robust Compressed Sensing MRI with Deep Generative Priors](https://mlsanity.com/paper/2108.01368/) (2021)
- [Brain Imaging Generation with Latent Diffusion Models](https://mlsanity.com/paper/2209.07162/) (2022)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Diffusion Models for Medical Anomaly Detection](https://mlsanity.com/paper/2203.04306/) (2022)
- [Gradient Magnitude Similarity Deviation: A Highly Efficient Perceptual Image Quality Index](https://mlsanity.com/paper/1308.3052/) (2013)
- [Improving Diffusion Inverse Problem Solving with Decoupled Noise Annealing](https://mlsanity.com/paper/2407.01521/) (2024)
- [Autoencoders for Unsupervised Anomaly Segmentation in Brain MR Images: A Comparative Study](https://mlsanity.com/paper/2004.03271/) (2020)
- [Score-Based Diffusion Models as Principled Priors for Inverse Imaging](https://mlsanity.com/paper/2304.11751/) (2023)
- [InverseBench: Benchmarking Plug-and-Play Diffusion Priors for Inverse Problems in Physical Sciences](https://mlsanity.com/paper/2503.11043/) (2025)
- [Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast](https://mlsanity.com/paper/2012.13340/) (2020)
- [Make-A-Volume: Leveraging Latent Diffusion Models for Cross-Modality 3D Brain MRI Synthesis](https://mlsanity.com/paper/2307.10094/) (2023)
- [Unsupervised 3D out-of-distribution detection with latent diffusion models](https://mlsanity.com/paper/2307.03777/) (2023)
- [Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting](https://mlsanity.com/paper/2403.14499/) (2024)
- [Denoising Diffusion Models for Inpainting of Healthy Brain Tissue](https://mlsanity.com/paper/2402.17307/) (2024)
- [Multi-Contrast MRI Reconstruction with Structure-Guided Total Variation](https://mlsanity.com/paper/1511.06631/) (2015)
- [Tackling Hallucination from Conditional Models for Medical Image Reconstruction with DynamicDPS](https://mlsanity.com/paper/2503.01075/) (2025)
- [MRI super-resolution reconstruction using efficient diffusion probabilistic model with residual shifting](https://mlsanity.com/paper/2503.01576/) (2025)
- [An Open-Source Tool for Longitudinal Whole-Brain and White Matter Lesion Segmentation](https://mlsanity.com/paper/2207.04534/) (2022)

## Abstract (arXiv)

Diffusion models have recently emerged as powerful generative models in medical imaging. However, it remains a major challenge to combine these data-driven models with domain knowledge to guide brain imaging problems. In neuroimaging, Bayesian inverse problems have long provided a successful framework for inference tasks, where incorporating domain knowledge of the imaging process enables robust performance without requiring extensive training data. However, the anatomical modeling component of these approaches typically relies on classical mathematical priors that often fail to capture the complex structure of brain anatomy. In this work, we present the first general-purpose application of diffusion models as priors for solving a wide range of medical imaging inverse problems. Our approach leverages a score-based diffusion prior trained extensively on diverse brain MRI data, paired with flexible forward models that capture common image processing tasks such as super-resolution, bias field correction, inpainting, and combinations thereof. We further demonstrate how our framework can refine outputs from existing deep learning methods to improve anatomical fidelity. Experiments on heterogeneous clinical and research MRI data show that our method achieves state-of-the-art performance producing consistent, high-quality solutions without requiring paired training datasets. These results highlight the potential of diffusion priors as versatile tools for brain MRI analysis.