TeamCoders_Event_Based_Model

This repository will hold all course content for the upcoming first iteration of the TeamCoders event. By the end of the project, attendees will:

1. Understand the concepts and steps of basic processing tasks behind imaging biomarkers
2. Practice standard data cleaning and visualization techniques to interrogate and investigate the input data before analysis.
3. Learn how to implement the Event Based Model with an application to reproduce findings from a seminal paper.
4. Further knowledge around the model’s outputs and utilize them for predicting future outcomes

Overview of format

This will be a team based learning event using Python notebooks. Teams will be provided with an introductory set of lectures and then will work independently at the problem, with daily check in sessions with the facilitators and experts. At the end of the third week, they will present their findings to the other teams and groups.

Prerequisites

If you are interested in attending this course or going through its content, then we would recommend:

• Basic familiarity with the Python programming language and
• Basic understanding of source code revision control using Git and Github
• Ensure you have access to ADNI data. If you do not already have access to the ADNI data set, please visit their Accessing data section to find out how to obtain access.
• Access to a machine with the following software:
  • Python via Anaconda or Miniconda - we provide an environment.yml file to create a conda environment with all of the core dependencies needed for this project. To set this environment up, type conda env create -f environment.yml in the top directory of this repository.
  • Image visualisation software - we will be using fsleyes when doing most of this work.
  • We would recommend having some other common neuroimaging software installed, primarily FSL and FreeSurfer.

Organisation of the repository

• There are four main parts to this project:
  1. Imaging biomarkers in AD
  2. Data cleaning and wrangling
  3. Using the EBM
  4. Interpreting and applying the EBM

Each part has its own folder, where you will find both the training content and blank notebooks for your team to fill in. Your team will forth this repository and start to fill in the notebooks.

Further Reading

In addition to the above repositories, to find out more about disease progression modelling, please view the DPM website which has further tutorials, examples and links.