# Diff-Def: Diffusion-Generated Deformation Fields for Conditional Atlases

arXiv: https://arxiv.org/abs/2403.16776 · HTML: https://mlsanity.com/paper/2403.16776/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 64 references that are in the map.
- First posted on arXiv 25 Mar 2024.

## Builds on (most cited first, 30 of 32)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [The Unreasonable Effectiveness of Deep Features as a Perceptual Metric](https://mlsanity.com/paper/1801.03924/) (2018)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Taming Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2012.09841/) (2020)
- [Improved Training of Wasserstein GANs](https://mlsanity.com/paper/1704.00028/) (2017)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [Diffusion Models in Vision: A Survey](https://mlsanity.com/paper/2209.04747/) (2022)
- [Which Training Methods for GANs do actually Converge?](https://mlsanity.com/paper/1801.04406/) (2018)
- [VoxelMorph: A Learning Framework for Deformable Medical Image Registration](https://mlsanity.com/paper/1809.05231/) (2018)
- [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)
- [Unsupervised Medical Image Translation with Adversarial Diffusion Models](https://mlsanity.com/paper/2207.08208/) (2022)
- [RoentGen: Vision-Language Foundation Model for Chest X-ray Generation](https://mlsanity.com/paper/2211.12737/) (2022)
- [A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images](https://mlsanity.com/paper/2209.13167/) (2022)
- [Conversion Between CT and MRI Images Using Diffusion and Score-Matching Models](https://mlsanity.com/paper/2209.12104/) (2022)
- [Generative AI for Medical Imaging: extending the MONAI Framework](https://mlsanity.com/paper/2307.15208/) (2023)
- [Learning Conditional Deformable Templates with Convolutional Networks](https://mlsanity.com/paper/1908.02738/) (2019)
- [Diffusion Deformable Model for 4D Temporal Medical Image Generation](https://mlsanity.com/paper/2206.13295/) (2022)
- [DiffuseMorph: Unsupervised Deformable Image Registration Using Diffusion Model](https://mlsanity.com/paper/2112.05149/) (2021)
- [Medical Diffusion: Denoising Diffusion Probabilistic Models for 3D Medical Image Generation](https://mlsanity.com/paper/2211.03364/) (2022)
- [What is Healthy? Generative Counterfactual Diffusion for Lesion Localization](https://mlsanity.com/paper/2207.12268/) (2022)
- [Mask, Stitch, and Re-Sample: Enhancing Robustness and Generalizability in Anomaly Detection through Automatic Diffusion Models](https://mlsanity.com/paper/2305.19643/) (2023)
- [Generation of Anonymous Chest Radiographs Using Latent Diffusion Models for Training Thoracic Abnormality Classification Systems](https://mlsanity.com/paper/2211.01323/) (2022)
- [Generative Adversarial Registration for Improved Conditional Deformable Templates](https://mlsanity.com/paper/2105.04349/) (2021)
- [A Novel Unified Conditional Score-based Generative Framework for Multi-modal Medical Image Completion](https://mlsanity.com/paper/2207.03430/) (2022)
- [FSDiffReg: Feature-wise and Score-wise Diffusion-guided Unsupervised Deformable Image Registration for Cardiac Images](https://mlsanity.com/paper/2307.12035/) (2023)
- [DreaMR: Diffusion-driven Counterfactual Explanation for Functional MRI](https://mlsanity.com/paper/2307.09547/) (2023)

## Built on by (most cited first, 8 of 8)

- [MultiMorph: On-demand Atlas Construction](https://mlsanity.com/paper/2504.00247/) (2025)
- [Guiding Registration with Emergent Similarity from Pre-Trained Diffusion Models](https://mlsanity.com/paper/2506.02419/) (2025)
- [Causal-Adapter: Taming Text-to-Image Diffusion for Faithful Counterfactual Generation](https://mlsanity.com/paper/2509.24798/) (2025)
- [Generating Novel Brain Morphology by Deforming Learned Templates](https://mlsanity.com/paper/2503.03778/) (2025)
- [An Efficient Model-Driven Groupwise Approach for Atlas Construction](https://mlsanity.com/paper/2508.10743/) (2025)
- [Multimodal Diffeomorphic Registration with Neural ODEs and Structural Descriptors](https://mlsanity.com/paper/2512.22689/) (2025)
- [Evaluating the Safety of Deep Learning-Based Brain MRI Reconstruction](https://mlsanity.com/paper/2608.28714/) (2026)
- [Geodesic-informed Generative Diffusion Model For Topology-preserved Image Video Generation](https://mlsanity.com/paper/2609.08153/) (2026)

## Abstract (arXiv)

Anatomical atlases are widely used for population studies and analysis. Conditional atlases target a specific sub-population defined via certain conditions, such as demographics or pathologies, and allow for the investigation of fine-grained anatomical differences like morphological changes associated with ageing or disease. Existing approaches use either registration-based methods that are often unable to handle large anatomical variations or generative adversarial models, which are challenging to train since they can suffer from training instabilities. Instead of generating atlases directly in as intensities, we propose using latent diffusion models to generate deformation fields, which transform a general population atlas into one representing a specific sub-population. Our approach ensures structural integrity, enhances interpretability and avoids hallucinations that may arise during direct image synthesis by generating this deformation field and regularising it using a neighbourhood of images. We compare our method to several state-of-the-art atlas generation methods using brain MR images from the UK Biobank. Our method generates highly realistic atlases with smooth transformations and high anatomical fidelity, outperforming existing baselines. We demonstrate the quality of these atlases through comprehensive evaluations, including quantitative metrics for anatomical accuracy, perceptual similarity, and qualitative analyses displaying the consistency and realism of the generated atlases.