Beyond FA

Building the Docker

To build this Docker container, clone the repository and run the following command in the root directory:

DOCKER_BUILDKIT=1 sudo docker build -t beyond_fa_pca:v0.0.5 .

The Docker runs the code from scripts/entrypoint.sh.

Running the Docker

Your Docker container should be able to read input data from /input and write output data to /output. Intermediate data should be written to /tmp. The input data will be a .mha file containing the diffusion MRI data with gradient table information contained in a .json file. The input file will be in /input/images/dwi-4d-brain-mri/, with gradient table information at /input/dwi-4d-acquisition-metadata.json. Your Docker should write a JSON list to the output directory with the name /output/features-128.json. Your JSON list must contain 128 values. You may zero-pad the list if you wish to provide fewer than 128 values.

To run this Docker:

input_dir=".../Inputs"
output_dir=".../Outputs"

mkdir -p $output_dir
sudo chmod 777 $output_dir

DOCKER_NOOP_VOLUME="beyond_fa_pca-volume"
sudo docker volume create "$DOCKER_NOOP_VOLUME" > /dev/null
sudo docker run \
    -it \
    --platform linux/amd64 \
    --network none \
    --gpus all \
    --rm \
    --volume $input_dir:/input:ro \
    --volume $output_dir:/output \
    --volume "$DOCKER_NOOP_VOLUME":/tmp \
    beyond_fa_pca:v0.0.5
sudo docker volume rm "$DOCKER_NOOP_VOLUME" > /dev/null