# White Matter Geometry-Guided Score-Based Diffusion Model for Tissue Microstructure Imputation in Tractography Imaging

arXiv: https://arxiv.org/abs/2407.19460 · HTML: https://mlsanity.com/paper/2407.19460/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 23 of its 41 references that are in the map.
- First posted on arXiv 28 Jul 2024.

## Placed in

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

## Builds on (most cited first, 23 of 23)

- [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)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [Maximum Likelihood Training of Score-Based Diffusion Models](https://mlsanity.com/paper/2101.09258/) (2021)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [GAIN: Missing Data Imputation using Generative Adversarial Nets](https://mlsanity.com/paper/1806.02920/) (2018)
- [Ensemble deep learning: A review](https://mlsanity.com/paper/2104.02395/) (2021)
- [Diffusion models for missing value imputation in tabular data](https://mlsanity.com/paper/2210.17128/) (2022)
- [DDM2: Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models](https://mlsanity.com/paper/2302.03018/) (2023)
- [AdvDiff: Generating Unrestricted Adversarial Examples using Diffusion Models](https://mlsanity.com/paper/2307.12499/) (2023)
- [Superficial White Matter Analysis: An Efficient Point-cloud-based Deep Learning Framework with Supervised Contrastive Learning for Consistent Tractography Parcellation across Populations and dMRI Acquisitions](https://mlsanity.com/paper/2207.08975/) (2022)
- [Model and predict age and sex in healthy subjects using brain white matter features: A deep learning approach](https://mlsanity.com/paper/2202.03595/) (2022)
- [Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation](https://mlsanity.com/paper/2107.04938/) (2021)
- [SupWMA: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning](https://mlsanity.com/paper/2201.12528/) (2022)
- [TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance](https://mlsanity.com/paper/2307.03982/) (2023)
- [TractGraphCNN: anatomically informed graph CNN for classification using diffusion MRI tractography](https://mlsanity.com/paper/2301.01911/) (2023)
- [TractoSCR: A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography](https://mlsanity.com/paper/2210.07411/) (2022)
- [Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods](https://mlsanity.com/paper/2306.05623/) (2023)
- [TractGraphFormer: Anatomically Informed Hybrid Graph CNN-Transformer Network for Interpretable Sex and Age Prediction from Diffusion MRI Tractography](https://mlsanity.com/paper/2407.08883/) (2024)
- [PPA: Principal Parcellation Analysis for Brain Connectomes and Multiple Traits](https://mlsanity.com/paper/2103.03478/) (2021)
- [Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes](https://mlsanity.com/paper/2303.09124/) (2023)
- [Cross-domain Fiber Cluster Shape Analysis for Language Performance Cognitive Score Prediction](https://mlsanity.com/paper/2403.19001/) (2024)
- [Imputing Brain Measurements Across Data Sets via Graph Neural Networks](https://mlsanity.com/paper/2308.09907/) (2023)

## Built on by (most cited first, 2 of 2)

- [The shape of the brain's connections is predictive of cognitive performance: an explainable machine learning study](https://mlsanity.com/paper/2410.15108/) (2024)
- [A Multimodal Deep Learning Approach for White Matter Shape Prediction in Diffusion MRI Tractography](https://mlsanity.com/paper/2504.18400/) (2025)

## Abstract (arXiv)

Parcellation of white matter tractography provides anatomical features for disease prediction, anatomical tract segmentation, surgical brain mapping, and non-imaging phenotype classifications. However, parcellation does not always reach 100% accuracy due to various factors, including inter-individual anatomical variability and the quality of neuroimaging scan data. The failure to identify parcels causes a problem of missing microstructure data values, which is especially challenging for downstream tasks that analyze large brain datasets. In this work, we propose a novel deep-learning model to impute tissue microstructure: the White Matter Geometry-guided Diffusion (WMG-Diff) model. Specifically, we first propose a deep score-based guided diffusion model to impute tissue microstructure for diffusion magnetic resonance imaging (dMRI) tractography fiber clusters. Second, we propose a white matter atlas geometric relationship-guided denoising function to guide the reverse denoising process at the subject-specific level. Third, we train and evaluate our model on a large dataset with 9342 subjects. Comprehensive experiments for tissue microstructure imputation and a downstream non-imaging phenotype prediction task demonstrate that our proposed WMG-Diff outperforms the compared state-of-the-art methods in both error and accuracy metrics. Our code will be available at: https://github.com/SlicerDMRI/WMG-Diff.