Brainhack Global 2021

IMaging-PsychiAtry Challenge (IMPAC): Predicting neurodevelopmental disorders from MRI data

Team

Iuliia Nikolaenko, Nicolas Traut , Franklin Leong, Despina Demenega, Inés Moreno, Baicai Ye, Juliette Faure, Fares Alouf, Marko Čuljak

Data

We merged two preprocessed datasets:

• The Autism Brain Imaging Data Exchange (ABIDE)
• Attention Deficit Hyperactivity Disorder (ADHD-200)

And indicated neurodevelopmental disorders in feature fx as 0 for control and 1 for diagnosed subjects. In dataset you will find the source of the data ABIDE/ADHD-200.

Getting started

This starting kit requires Python and the following dependencies:

• numpy<1.20
• scipy
• pandas>=0.21
• scikit-learn>=0.19,<=0.21
• matplolib
• seaborn
• nilearn
• jupyter
• ramp-workflow==0.2.1

Therefore, we advise you to install Anaconda distribution which include almost all dependencies.

Only nilearn and ramp-workflow are not included by default in the Anaconda distribution. They will be installed from the execution of the notebook.

Execute the jupyter notebook, from the root directory using:

jupyter notebook neurodevelop_starting_kit.ipynb

Advanced install using conda (optional)

We provide both an environment.yml file which can be used with conda to create a clean environment and install the necessary dependencies.

conda env create -f environment.yml

Then, you can activate the environment using:

conda activate neurodevelop

for Linux and MacOS. In Windows, use the following command instead:

activate neurodevelop