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Docker Setup

Brief walkthrough on how to prepare the autoafids_prep package in a Docker container.

Local Build Instructions

To build a docker image of the project locally, do the following:

  1. Download the git repo:
git clone https://github.com/afids/autoafids_prep.git

  1. Ensure you have installed Docker and that it's up and running.

  2. Build the docker image using the following command; it should be executed within the repository folder (i.e., autoafids_prep/).

docker build -t autoafids_prep:<VERSION> -f ./docker/Dockerfile .
  1. Once the image is built, you can then run the pipeline as follows:
docker run -it --rm \                     
-v local/path/to/dataset:/bids_dataset \ 
-v local/path/to/dataset/derivatives:/output \  
autoafids_prep:<VERSION> \
/bids_dataset /output participant --cores all

The first time building this image may take some time because poetry takes a while to install all the required python packages.