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README.md

README.md

How is experience transformed into memory?

This repository contains data and code used to produce the paper "How is experience transformed into memory" by Andrew C. Heusser, Paxton C. Fitzpatrick, and Jeremy R. Manning. The repository is organized as follows:

root
└── code : all code used in the paper
    ├── notebooks : jupyter notebooks for paper analyses
    └── scripts : python scripts used to perform brain searchlight analyses on a cluster
└── data : all data used in the paper
    ├── raw : raw data before processing
    └── processed : all processed data
└── paper : all files to generate paper
    └── figs : pdf copies of each figure

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 sherlock .
  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 Sherlock -v ~/Desktop:/mnt sherlock
    • 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 Sherlock && docker attach Sherlock
    • 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 Sherlock from any other terminal