Deformation-Based Morphometry using Deep Learning

Keywords: Deformation-Based Morphometry, Normal Aging, Alzheimer’s Disease, Deep Learning, Brain Morphology

This repository contains the source code accompanying the paper:

Fu, Jingru, et al. "Decomposing the effect of normal aging and Alzheimer’s disease in brain morphological changes via learned aging templates", Scientific Reports, 2025.

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TODOs

• Add the link to the paper
• Share the pre-trained weights (in ./models)
• Add the Jupyter notebook demo (step-by-step_example.ipynb)

OASIS-3 Dataset

We used the OASIS-3 dataset in this project. To preprocess the data in accordance with our study, please refer to https://github.com/Fjr9516/Nii2NPZ.

If you use this dataset, please cite the following and refer to the corresponding Data Use Agreement .

• OASIS-3: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer Disease. Pamela J LaMontagne, Tammie L.S. Benzinger, John C. Morris, Sarah Keefe, Russ Hornbeck, Chengjie Xiong, Elizabeth Grant, Jason Hassenstab, Krista Moulder, Andrei Vlassenko, Marcus E. Raichle, Carlos Cruchaga, Daniel Marcus, 2019. medRxiv. doi: 10.1101/2019.12.13.19014902

Pre-trained Healthy Template Creation Models

We offer pretrained Atlas-GAN weights trained on the OASIS-3 Dataset for simulating normal aging. Additionally, we provide inference scripts for extracting the learned diffeomorphic registration module and template generation module. (in ./models)

The extracted healthy templates are also available in NIfTI format, spanning ages from 60 to 90. (in ./example/CN_templates)

Citation

@article{fu2025decomposing,
  title={Decomposing the effect of normal aging and Alzheimer’s disease in brain morphological changes via learned aging templates},
  author={Fu, Jingru and Ferreira, Daniel and Smedby, {\"O}rjan and Moreno, Rodrigo},
  journal={Scientific Reports},
  volume={15},
  number={1},
  pages={11813},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@misc{fu2023deformationbased,
      title={A deformation-based morphometry framework for disentangling Alzheimer's disease from normal aging using learned normal aging templates}, 
      author={Jingru Fu and Daniel Ferreira and Örjan Smedby and Rodrigo Moreno},
      year={2023},
      eprint={2311.08176},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

Acknowledgements:

This repository is developed based on the Atlas-GAN project and makes extensive use of the VoxelMorph library.