mlsanityData to 14 Oct 2026

Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting

arXiv 2403.14499 ↗First posted 21 Mar 2024eess.IV cs.CVcited by 22

On the map: Diffusion models → Medical imaging and segmentation

Abstract (arXiv)

Monitoring diseases that affect the brain's structural integrity requires automated analysis of magnetic resonance (MR) images, e.g., for the evaluation of volumetric changes. However, many of the evaluation tools are optimized for analyzing healthy tissue. To enable the evaluation of scans containing pathological tissue, it is therefore required to restore healthy tissue in the pathological areas. In this work, we explore and extend denoising diffusion models for consistent inpainting of healthy 3D brain tissue. We modify state-of-the-art 2D, pseudo-3D, and 3D methods working in the image space, as well as 3D latent and 3D wavelet diffusion models, and train them to synthesize healthy brain tissue. Our evaluation shows that the pseudo-3D model performs best regarding the structural-similarity index, peak signal-to-noise ratio, and mean squared error. To emphasize the clinical relevance, we fine-tune this model on data containing synthetic MS lesions and evaluate it on a downstream brain tissue segmentation task, whereby it outperforms the established FMRIB Software Library (FSL) lesion-filling method.

Key facts. Cited by 22 papers in the map (data through 14 Oct 2026). Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models. Builds on 26 of its 37 references that are in the map. First posted on arXiv 21 Mar 2024.

Builds on

26 of 37 references.

Closest ancestors · 8

Same direction, newest first

  1. 2024WDM: 3D Wavelet Diffusion Models for High-Resolution Medical Image Synthesis29 Feb
  2. 2024Denoising Diffusion Models for Inpainting of Healthy Brain Tissue27 Feb
  3. 2023Make-A-Volume: Leveraging Latent Diffusion Models for Cross-Modality 3D Brain MRI Synthesis19 Jul
  4. 2023Memory-Efficient 3D Denoising Diffusion Models for Medical Image Processing27 Mar
  5. 2023Diffusion Models for Contrast Harmonization of Magnetic Resonance Images14 Mar
  6. 2022Medical Diffusion: Denoising Diffusion Probabilistic Models for 3D Medical Image Generation7 Nov
  7. 2022Diffusion Models for Medical Anomaly Detection8 Mar
  8. 2021Diffusion Models for Implicit Image Segmentation Ensembles6 Dec

Other references · 18

  1. 2020Denoising Diffusion Probabilistic Modelscited by 21,076
  2. 2021High-Resolution Image Synthesis with Latent Diffusion Modelscited by 18,863
  3. 2021Diffusion Models Beat GANs on Image Synthesiscited by 8,255
  4. 2017Neural Discrete Representation Learningcited by 4,712
  5. 2021Improved Denoising Diffusion Probabilistic Modelscited by 3,761
  6. 2022Elucidating the Design Space of Diffusion-Based Generative Modelscited by 3,045
  7. 2022RePaint: Inpainting using Denoising Diffusion Probabilistic Modelscited by 1,430
  8. 2019Generating Diverse High-Fidelity Images with VQ-VAE-2cited by 1,387
  9. 2021Palette: Image-to-Image Diffusion Modelscited by 1,300
  10. 2021Resolution-robust Large Mask Inpainting with Fourier Convolutionscited by 738
  11. 2018Generative Image Inpainting with Contextual Attentioncited by 580
  12. 2021The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classificationcited by 518
6 more
  1. 2018Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challengecited by 511
  2. 2022Wavelet Diffusion Models are fast and scalable Image Generatorscited by 117
  3. 2021Generating Diverse Structure for Image Inpainting With Hierarchical VQ-VAEcited by 106
  4. 2021Aggregated Contextual Transformations for High-Resolution Image Inpaintingcited by 89
  5. 2021MedPerf: Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluationcited by 88
  6. 2023Point Cloud Diffusion Models for Automatic Implant Generationcited by 19

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2024: 4; 2025: 11; 2026: 7.

22 papers.

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  1. 2024Deep Generative Models for 3D Medical Image Synthesiscited by 14
  2. 2025Regression is all you need for medical image translationcited by 8
  3. 2025fastWDM3D: Fast and Accurate 3D Healthy Tissue Inpaintingcited by 8
  4. 2024Denoising Plane Wave Ultrasound Images Using Diffusion Probabilistic Modelscited by 6
  5. 2025Conditional diffusion models for guided anomaly detection in brain images using fluid-driven anomaly randomizationcited by 6
  6. 2024Brain Tumour Removing and Missing Modality Generation using 3D WDMcited by 4
  7. 2024Denoising Diffusion Models for Anomaly Localization in Medical Imagescited by 3
  8. 2025DiffKAN-Inpainting: KAN-based Diffusion model for brain tumor inpaintingcited by 3
  9. 2025High Volume Rate 3D Ultrasound Reconstruction with Diffusion Modelscited by 2
  10. 2025RealDeal: Enhancing Realism and Details in Brain Image Generation via Image-to-Image Diffusion Modelscited by 1
  11. 2025Towards MR-Based Trochleoplasty Planningcited by 1
  12. 2025Exploring Robustness of Cortical Morphometry in the presence of white matter lesions, using Diffusion Models for Lesion Fillingcited by 0
10 more
  1. 20253D Shape Generation: A Surveycited by 0
  2. 2025Deep generative priors for 3D brain analysiscited by 0
  3. 2025BrainNormalizer: Anatomy-Informed Pseudo-Healthy Brain Reconstruction from Tumor MRI via Edge-Guided ControlNetcited by 0
  4. 2026Kidney Cancer Detection Using 3D-Based Latent Diffusion Modelscited by 0
  5. 2026POWDR: Pathology-preserving Outpainting with Wavelet Diffusion for 3D MRIcited by 0
  6. 2026Longitudinal Lesion Inpainting in Brain MRI via 3D Region Aware Diffusioncited by 0
  7. 2026Diffusion Models in Medical Image Inpainting: Challenges, Solution Taxonomy, and Future Directionscited by 0
  8. 2026Now You Have My Healthy Attention: A U-DiT for Brain-MRI Inpaintingcited by 0
  9. 2026RARF: Region-Aware Rectified Flows for 3D Brain MRI Inpaintingcited by 0
  10. 2026CATCH: Counterfactual Anatomical Tissue Inpainting with Conditional Haar Diffusioncited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2025Hierarchical Diffusion Framework for Pseudo-Healthy Brain MRI Inpainting with Enhanced 3D Consistency
  2. 2023Denoising Diffusion Probabilistic Models for Image Inpainting of Cell Distributions in the Human Brain
  3. 2024On Instabilities of Unsupervised Denoising Diffusion Models in Magnetic Resonance Imaging Reconstruction
  4. 2022Diffusion Models for Medical Image Analysis: A Comprehensive Survey
  5. 2026Improving 2D Diffusion Models for 3D Medical Imaging with Inter-Slice Consistent Stochasticity
  6. 2025Computationally Efficient Diffusion Models in Medical Imaging: A Comprehensive Review
  7. 2022The Swiss Army Knife for Image-to-Image Translation: Multi-Task Diffusion Models
  8. 2025A Biophysically-Conditioned Generative Framework for 3D Brain Tumor MRI Synthesis