initial molerat template build script

examples/molerat/3_build_template.sh

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+#!/bin/bash
+
+# Start the timer
+start_time=$(date +%s)
+
+# Initialize CLI parameters with default values
+average_type="mean"
+
+# Function to display help message
+usage() {
+  echo "Usage: $0 --atlas-dir <path> --template-name <string> [--average-type <string>]"
+  echo ""
+  echo "Options:"
+  echo "  --atlas-dir <path>         Path to the atlas-forge directory [REQUIRED]"
+  echo "  --template-name <string>   The name of the appropriate subfolder within templates (e.g., template_asym_res-50um_n-8) [REQUIRED]"
+  echo "  --average-type <string>    The type of average to use (default: mean)."
+  exit 1
+}
+
+# Check for help flag first
+if [[ "$1" == "--help" ]]; then
+  usage
+fi
+
+# Parse command line arguments
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    --atlas-dir)
+      atlas_dir="$2"
+      shift 2
+      ;;
+    --template-name)
+      template_name="$2"
+      shift 2
+      ;;
+    --average-type)
+      average_type="$2"
+      shift 2
+      ;;
+    --help)
+      usage
+      ;;
+    *)
+      echo "Unknown option $1"
+      usage
+      ;;
+  esac
+done
+
+# Check for required parameters
+if [ -z "$atlas_dir" ] || [ -z "$template_name" ]; then
+  echo "Error: --atlas-dir and --template-name are required."
+  usage
+fi
+
+echo "atlas-dir: ${atlas_dir}"
+echo "Building the template ${template_name}..."
+
+# Set the path to the working directory where the template will be built
+templates_dir="${atlas_dir}/templates"
+working_dir="${templates_dir}/${template_name}"
+
+# If average type is trimmed_mean or efficient_trimean, we need python
+average_prog="ANTs"
+if [ "${average_type}" == "trimmed_mean" ] || [ "${average_type}" == "efficient_trimean" ]; then
+  average_prog="python"
+fi
+
+# Verify that the working directory exists before changing directory
+if [ ! -d "${working_dir}" ]; then
+  echo "The working directory does not exist: ${working_dir}"
+  exit 1
+fi
+
+cd "${working_dir}" || exit
+
+echo "Results will be written to ${working_dir}"
+
+# Execute the actual template building
+echo "Starting to build the template..."
+bash modelbuild.sh --output-dir "${working_dir}" \
+    --starting-target first \
+    --stages rigid,similarity,affine,nlin \
+    --masks "${working_dir}/mask_paths.txt" \
+    --average-type "${average_type}" \
+    --average-prog "${average_prog}" \
+    --reuse-affines \
+    --dry-run \
+    "${working_dir}/brain_paths.txt"
+
+echo "Finished building the template!"
+
+# Write execution time (in HH:MM format) to a file
+end_time=$(date +%s)
+execution_time=$((end_time - start_time))
+hours=$((execution_time / 3600))
+minutes=$(( (execution_time % 3600) / 60))
+formatted_time=$(printf "%02d:%02d" $hours $minutes)
+echo "Execution time: $formatted_time" > "${working_dir}/execution_time.txt"