# Exploring Robustness of Cortical Morphometry in the presence of white matter lesions, using Diffusion Models for Lesion Filling

arXiv: https://arxiv.org/abs/2503.20571 · HTML: https://mlsanity.com/paper/2503.20571/

## 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 17 of its 44 references that are in the map.
- First posted on arXiv 26 Mar 2025.

## Placed in

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

## Builds on (most cited first, 17 of 17)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [The Unreasonable Effectiveness of Deep Features as a Perceptual Metric](https://mlsanity.com/paper/1801.03924/) (2018)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [RePaint: Inpainting using Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2201.09865/) (2022)
- [Resolution-robust Large Mask Inpainting with Fourier Convolutions](https://mlsanity.com/paper/2109.07161/) (2021)
- [Free-Form Image Inpainting with Gated Convolution](https://mlsanity.com/paper/1806.03589/) (2018)
- [Image Inpainting for Irregular Holes Using Partial Convolutions](https://mlsanity.com/paper/1804.07723/) (2018)
- [Efficient Diffusion Training via Min-SNR Weighting Strategy](https://mlsanity.com/paper/2303.09556/) (2023)
- [FastSurfer -- A fast and accurate deep learning based neuroimaging pipeline](https://mlsanity.com/paper/1910.03866/) (2019)
- [High-Resolution Image Inpainting with Iterative Confidence Feedback and Guided Upsampling](https://mlsanity.com/paper/2005.11742/) (2020)
- [Make-A-Volume: Leveraging Latent Diffusion Models for Cross-Modality 3D Brain MRI Synthesis](https://mlsanity.com/paper/2307.10094/) (2023)
- [Memory-Efficient 3D Denoising Diffusion Models for Medical Image Processing](https://mlsanity.com/paper/2303.15288/) (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)

## Abstract (arXiv)

Cortical thickness measurements from magnetic resonance imaging, an important biomarker in many neurodegenerative and neurological disorders, are derived by many tools from an initial voxel-wise tissue segmentation. White matter (WM) hypointensities in T1-weighted imaging, such as those arising from multiple sclerosis or small vessel disease, are known to affect the output of brain segmentation methods and therefore bias cortical thickness measurements. These effects are well-documented among traditional brain segmentation tools but have not been studied extensively in tools based on deep-learning segmentations, which promise to be more robust. In this paper, we explore the potential of deep learning to enhance the accuracy and efficiency of cortical thickness measurement in the presence of WM lesions, using a high-quality lesion filling algorithm leveraging denoising diffusion networks. A pseudo-3D U-Net architecture trained on the OASIS dataset to generate synthetic healthy tissue, conditioned on binary lesion masks derived from the MSSEG dataset, allows realistic removal of white matter lesions in multiple sclerosis patients. By applying morphometry methods to patient images before and after lesion filling, we analysed robustness of global and regional cortical thickness measurements in the presence of white matter lesions. Methods based on a deep learning-based segmentation of the brain (Fastsurfer, DL+DiReCT, ANTsPyNet) exhibited greater robustness than those using classical segmentation methods (Freesurfer, ANTs).