BUG: Fix ShellCheck issues

example_run_brain_mask_tool_docker.sh

@@ -1,30 +1,36 @@
 #!/bin/bash
-CURRENT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )  # Get the directory of the script
+
+# Get the directory of the script
+CURRENT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
 # Default values
 DEFAULT_INPUT_DIR="${CURRENT_DIR}/example_tool/example_data/CAIPIRINHA_SPACE_Neuro_Head_Examples"
 DEFAULT_OUTPUT_DIR="${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}
+INPUT_DIR=${1:-"${DEFAULT_INPUT_DIR}"}
+OUTPUT_DIR=${2:-"${DEFAULT_OUTPUT_DIR}"}
+STUDY_ID=${3:-"${DEFAULT_STUDY_ID}"}
 
-if [ ! -d "$INPUT_DIR" ]; then
-  echo "Input directory does not exist: $INPUT_DIR"
+# Check if input directory exists
+if [ ! -d "${INPUT_DIR}" ]; then
+  echo "Input directory does not exist: ${INPUT_DIR}"
   exit 1
 fi
-if [ ! -d "$OUTPUT_DIR" ]; then
-  echo "Output directory does not exist: $OUTPUT_DIR"
-  echo "Creating output directory: $OUTPUT_DIR"
-  mkdir -p "$OUTPUT_DIR"
-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:v0.1\
+-v "${INPUT_DIR}":/input \
+-v "${OUTPUT_DIR}":/output \
+brainmasktool:v0.1 \
  -s /input \
- -o /output\
- -i "$STUDY_ID"
+ -o /output \
+ -i "${STUDY_ID}"