example_run_brain_mask_tool_docker.sh

#!/bin/bash

# Get the directory of the script
CURRENT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )

# Default values
DEFAULT_INPUT_DIR="${CURRENT_DIR}/example_data/CAIPIRINHA_SPACE_Neuro_Head_Examples"
DEFAULT_OUTPUT_DIR="${CURRENT_DIR}/example_tool/example_output"
DEFAULT_STUDY_ID="12345"

# Use provided arguments if they exist, otherwise use default values
INPUT_DIR=${1:-"${DEFAULT_INPUT_DIR}"}
OUTPUT_DIR=${2:-"${DEFAULT_OUTPUT_DIR}"}
STUDY_ID=${3:-"${DEFAULT_STUDY_ID}"}

# Check if input directory exists
if [ ! -d "${INPUT_DIR}" ]; then
  echo "Input directory does not exist: ${INPUT_DIR}"
  exit 1
fi

# Check if output directory exists, if not create it
if [ ! -d "${OUTPUT_DIR}" ]; then
  echo "Output directory does not exist: ${OUTPUT_DIR}"
  echo "Creating output directory: ${OUTPUT_DIR}"
  mkdir -p "${OUTPUT_DIR}"
fi

# Run the docker command
docker run --rm \
-v "${INPUT_DIR}":/input \
-v "${OUTPUT_DIR}":/output \
brainmasktool \
 -s /input \
 -o /output \
 -i "${STUDY_ID}"