# BrainMRDiff: A Diffusion Model for Anatomically Consistent Brain MRI Synthesis

arXiv: https://arxiv.org/abs/2504.04532 · HTML: https://mlsanity.com/paper/2504.04532/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 61 of its 83 references that are in the map.
- First posted on arXiv 6 Apr 2025.

## Placed in

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

## Builds on (most cited first, 30 of 61)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Adding Conditional Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.05543/) (2023)
- [DreamBooth: Fine Tuning Text-to-Image Diffusion Models for Subject-Driven Generation](https://mlsanity.com/paper/2208.12242/) (2022)
- [T2I-Adapter: Learning Adapters to Dig out More Controllable Ability for Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.08453/) (2023)
- [Semantic Image Synthesis with Spatially-Adaptive Normalization](https://mlsanity.com/paper/1903.07291/) (2019)
- [GLIGEN: Open-Set Grounded Text-to-Image Generation](https://mlsanity.com/paper/2301.07093/) (2023)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Uni-ControlNet: All-in-One Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2305.16322/) (2023)
- [Follow Your Pose: Pose-Guided Text-to-Video Generation using Pose-Free Videos](https://mlsanity.com/paper/2304.01186/) (2023)
- [Composer: Creative and Controllable Image Synthesis with Composable Conditions](https://mlsanity.com/paper/2302.09778/) (2023)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Diffusion Models for Medical Image Analysis: A Comprehensive Survey](https://mlsanity.com/paper/2211.07804/) (2022)
- [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)
- [Statistical Aspects of Wasserstein Distances](https://mlsanity.com/paper/1806.05500/) (2018)
- [UniControl: A Unified Diffusion Model for Controllable Visual Generation In the Wild](https://mlsanity.com/paper/2305.11147/) (2023)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [Listen, Denoise, Action! Audio-Driven Motion Synthesis with Diffusion Models](https://mlsanity.com/paper/2211.09707/) (2022)
- [MedSegDiff: Medical Image Segmentation with Diffusion Probabilistic Model](https://mlsanity.com/paper/2211.00611/) (2022)
- [DiffTalk: Crafting Diffusion Models for Generalized Audio-Driven Portraits Animation](https://mlsanity.com/paper/2301.03786/) (2023)
- [Consistent View Synthesis with Pose-Guided Diffusion Models](https://mlsanity.com/paper/2303.17598/) (2023)
- [Advancing Pose-Guided Image Synthesis with Progressive Conditional Diffusion Models](https://mlsanity.com/paper/2310.06313/) (2023)

## Built on by (most cited first, 4 of 4)

- [Learning Patient-Specific Disease Dynamics with Latent Flow Matching for Longitudinal Imaging Generation](https://mlsanity.com/paper/2512.09185/) (2025)
- [Anatomy-DT: A Cross-Diffusion Digital Twin for Anatomical Evolution](https://mlsanity.com/paper/2509.25280/) (2025)
- [SoC-DT: Standard-of-Care Aligned Digital Twins for Patient-Specific Tumor Dynamics](https://mlsanity.com/paper/2510.03287/) (2025)
- [AnaDiffusion: Anatomically CompositionalLatent Diffusion for Controllable 3D Brain MRI Generation](https://mlsanity.com/paper/2608.23014/) (2026)

## Abstract (arXiv)

Accurate brain tumor diagnosis relies on the assessment of multiple Magnetic Resonance Imaging (MRI) sequences. However, in clinical practice, the acquisition of certain sequences may be affected by factors like motion artifacts or contrast agent contraindications, leading to suboptimal outcome, such as poor image quality. This can then affect image interpretation by radiologists. Synthesizing high quality MRI sequences has thus become a critical research focus. Though recent advancements in controllable generative AI have facilitated the synthesis of diagnostic quality MRI, ensuring anatomical accuracy remains a significant challenge. Preserving critical structural relationships between different anatomical regions is essential, as even minor structural or topological inconsistencies can compromise diagnostic validity. In this work, we propose BrainMRDiff, a novel topology-preserving, anatomy-guided diffusion model for synthesizing brain MRI, leveraging brain and tumor anatomies as conditioning inputs. To achieve this, we introduce two key modules: Tumor+Structure Aggregation (TSA) and Topology-Guided Anatomy Preservation (TGAP). TSA integrates diverse anatomical structures with tumor information, forming a comprehensive conditioning mechanism for the diffusion process. TGAP enforces topological consistency during reverse denoising diffusion process; both these modules ensure that the generated image respects anatomical integrity. Experimental results demonstrate that BrainMRDiff surpasses existing baselines, achieving performance improvements of 23.33% on the BraTS-AG dataset and 33.33% on the BraTS-Met dataset. Code will be made publicly available soon.