This is a repository for a ultra-high-resolution 7T study in the Knapen lab (https://tknapen.github.io/).
All the analysis in this repository can (should) be run using the included Docker image.
You need to install Docker on your MacBook/server/workstation. See here for instructions
To run the docker image, do the following:
- First, clone this repository:
git clone https://github.com/VU-Cog-Sci/hires_ODC_7T
- Then, build the Docker image (this will take a while, but has to be done only once):
docker build . -t "knapenlab/hiresbinocularrivalry"
You now can run the Docker, it is important that you specify the path where the relevant data can be found:
export DATA_PATH="/path/to/the/data"
- There are multiple ways to run the docker. By default, the image starts a Jupyter Notebook server:
docker run -it -p 8888:8888 -v $DATA_PATH:/data knapenlab/hiresbinocularrivalry
When you are developing, it can be useful to link /home/neuro/notebooks and/or /home/neuro/src to folders on the host machine. You can do that as follows:
docker run -P -it -v DATA_PATH:/data knapenlab/hiresbinocularrivalry \
-v /path/to/notebooks/:/home/neuro/notebooks \
-v /path/to/src/:/home/neuro/src
You can now open the Jupyter Notebook using your favorite browser (Chrome) with the following URL: http://localhost:8888/
- Another option is to start a (z)shell and peek around yourself
docker run -it -v $DATA_PATH:/data knapenlab/hiresbinocularrivalry zsh
In principle, this Docker image can be started using Jupyterhub in a similar way as the standard https://github.com/jupyter/docker-stacks.
- Lastly, an experimental feature is to stary jupyter-lab
docker run -it -p 8888:8888 -v $DATA_PATH:/data knapenlab/hiresbinocularrivalry jupyter-lab