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README.md

README.md

A Gaussian process model of human electrocorticographic data

This repository contains data and code used to produce our "SuperEEG" paper, by Lucy L. W. Owen, Andrew C. Heusser, and Jeremy R. Manning, entitled "A Gaussian process model of human electrocorticographic data." If you are looking to apply SuperEEG to your own ECoG data, you may also be interested in our SuperEEG Python Toolbox.

This repository is organized as follows:

root
└── code : all code used in the paper
    └── scripts : python scripts used to perform pyfr analyses on a cluster
    └── notebooks : jupyter notebooks for paper analyses and paper figures
└── data : processed data
    ├── pyfr : compiled reconstruction accuracy from pyfr ("Dataset 1") analyses
    └── ram : compiled reconstruction accuracy from ram ("Dataset 2") analyses
└── paper : all latex and pdf files to generate paper
    └── figs : all final pdfs

We also include a Dockerfile to reproduce our computational environment. Instruction for use are below (copied and modified from MIND repo):

One time setup

  1. Install Docker on your computer using the appropriate guide below:
  2. Launch Docker and adjust the preferences to allocate sufficient resources (e.g. > 4GB RAM)
  3. Build the docker image by opening a terminal in this repo folder and enter docker build -t supereeg .
  4. Use the image to create a new container for the workshop
    • The command below will create a new container that will map your computer's Desktop to /mnt within the container, so that location is shared between your host OS and the container. Feel free to change Desktop to whatever folder you prefer to share instead, but make sure to provide the full path. The command will also share port 9999 with your host computer so any jupyter notebooks launched from within the container will be accessible at localhost:9999 in your web browser
    • docker run -it -p 9999:9999 --name Supereeg -v ~/Desktop:/mnt supereeg
    • You should now see the root@ prefix in your terminal, if so you've successfully created a container and are running a shell from inside!
  5. To launch any of the notebooks: jupyter lab --port=9999 --no-browser --ip=0.0.0.0 --allow-root

Using the container after setup

  1. You can always fire up the container by typing the following into a terminal
    • docker start Supereeg && docker attach Supereeg
    • When you see the root@ prefix, letting you know you're inside the container
  2. Close a running container with ctrl + d from the same terminal you used to launch the container, or docker stop Supereeg from any other terminal