cbinyu/cbi_pydeface repository overview

⁠cbi_pydeface

Code to build a Docker image of poldracklab's pydeface tool (github.com/poldracklab/pydeface).

⁠Get the docker image

To get the Docker image (recommended --much faster), run:

docker pull cbinyu/cbi_pydeface

To build the image yourself:

git clone https://github.com/cbinyu/cbi_pydeface.git
cd cbi_pydeface
docker build -t cbi_pydeface .

It will build a temporary image and a final image, which is a slim-down version of the temporary one.

⁠Run pydeface on Docker:

To run pydeface on an image, follow the instructions for the command-line tool (github.com/poldracklab/pydeface), replacing pydeface with docker run cbinyu/cbi_pydeface (if you pull the Docker image) or docker run cbi_pydeface (if you built it). E.g.:

docker run cbinyu/cbi_pydeface infile.nii.gz

Notes:

• You need to pass the path to infile inside the Docker container. This might involve mounting some host drive in the Docker container.
• It is recommended that you run your Docker containers as a user different from root (default). E.g., to use the same user and group IDs that you have in your host machine, run:

docker run --user $UID:$(id -g $UID) cbinyu/cbi_pydeface infile.nii.gz