This repository contains data and code used to produce our "SuperEEG" paper, by Lucy L. W. Owen, Tudor A. Muntianu, Andrew C. Heusser, Patrick Daly, Katherine Scangos, and Jeremy R. Manning, entitled "A Gaussian process model of human electrocorticographic data" in press at Cerebral Cortex. 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):
- Install Docker on your computer using the appropriate guide below:
- Launch Docker and adjust the preferences to allocate sufficient resources (e.g. > 4GB RAM)
- Build the docker image by opening a terminal in this repo folder and enter
docker build -t supereeg .
- 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 changeDesktop
to whatever folder you prefer to share instead, but make sure to provide the full path. The command will also share port9999
with your host computer so any jupyter notebooks launched from within the container will be accessible atlocalhost: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!
- The command below will create a new container that will map your computer's
- To launch any of the notebooks:
jupyter lab --port=9999 --no-browser --ip=0.0.0.0 --allow-root
- 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
- Close a running container with
ctrl + d
from the same terminal you used to launch the container, ordocker stop Supereeg
from any other terminal