adai

An AI for pre-diagnosing Alzheimer's Disease.

Prerequisites

It is recommend to run the notebooks with a python3 conda environment (i.e. anaconda, miniconda, etc.)

Follow the instructions on the pytorch website to install pytorch. Then, after activating the conda env run:

pip install -r requirements.txt

Getting Data

You can request access to the data here. Make sure you request the OASIS 3 brains dataset. Download the data in the plain folder format. Once you get the Pib PET/MRI data, put it anywhere you like (ideally in the same folder as this repo) and change the DATA_DIR variable in the notebook you wish to use. Also, make sure to get the diagnosis of the patients by clicking on the "spreadsheet" value on data explorer.

Notebooks

Notebook Name	Description
mri_3d_resnet_pretrained.ipynb	3D residual neural network trained on MRI data, pretrained on MedicalNet
pet_3d_resnet_with_linear_pretrained.ipynb	3D residual neural network trained on PET data, pretrained on MedicalNet, uses linear layers for the collection of 3D frames
pet_3d_resnet_with_linear.ipynb	3D residual neural network trained on PET data, uses linear layers for the collection of 3D frames
pet_3d_resnet_with_lstm.ipynb	3D residual neural network trained on PET data, uses lstm layers for the collection of 3D frames