zapaishchykova / SynthBrainGrow

Repo for the paper "SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People"

SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People

This directory for the code for the paper "SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People" Arxiv

Requirements

To run the example, you will need to install the MONAI Generative Models package, matplotlib and Jupyter Notebook. pip install monai-generative

Data

Since ABCD dataset needs to be formaly requested, we demonstrate the feasibility of the pipeline on the OpenNeuro Dataset "A longitudinal neuroimaging dataset on language processing in children ages 5, 7, and 9 years old". We will only use pairs of images that were recorded at 7-9 years old, since method was initially trained on 8-16 years old subjects from ABCD dataset.

Note: since this dataset requires N4 debiasing, it will take a while to preprocess all.

Running the example

Prerequisites: conda, gpu

To run the example, you will need to run the Jupyter Notebook. This can be done by running the following command:

jupyter notebook

And open inference.ipynb in the browser.

Citation

If you use this code, please cite the following paper:

@article{zapaishchykova2024synthbraingrow,
  title={SynthBrainGrow: Synthetic Diffusion Brain Aging for Longitudinal MRI Data Generation in Young People},
  author={Zapaishchykova, Anna and Kann, Benjamin H and Tak, Divyanshu and Ye, Zezhong and Haas-Kogan, Daphne A and Aerts, Hugo JWL},
  journal={arXiv preprint arXiv:2405.00682},
  year={2024}
}

Work in progress

This repository is a work in progress. [x] Add example notebook for inference and data processing [x] Add model weights [x] Add readme [x] Add example data [] Add example notebook for training [] Add more details on enviroment creation [] Create Docker container for easy deployment

LICENSE: CC BY-NC 4.0

This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. Copyright (c) [2023] [Diffusion Deep Learning for Brain Age Prediction and Longitudinal Tracking in Children though Adulthood]