[DATALAD] Recorded changes

Author: synchon

xfm_generation.sh

@@ -0,0 +1,128 @@
+#!/usr/bin/env bash
+
+# Generates template space transformation assets via ANTs
+#
+# Synchon Mandal 2024, Forschungszentrum Juelich GmbH
+
+# Exit when a command fails
+set -o errexit
+# Fail when accessing unset variables
+set -o nounset
+# Fail when even one command in pipeline fails
+set -o pipefail
+# Allow debug by using `TRACE=1 ./xfm_generation.sh`
+[[ "${TRACE-0}" == "1" ]] && set -o xtrace
+
+# Help command
+if [[ "${1-}" =~ ^-*h(elp)?$ ]]; then
+    cat <<USAGE
+
+Generates human template space transformation assets via ANTs. Template space
+names are according to `templateflow <https://www.templateflow.org/browse/>`
+without the `tpl-`.
+
+Usage:
+
+  ./xfm_generation.sh -f <src-template-space-t1w> -t <target-template-space-t1w>
+
+    -f <src-template-space-t1w>    Source template space (e.g., MNI152NLin2009cAsym)
+    -t <target-template-space-t1w> Target template space (e.g., MNI152NLin6Asym)
+
+USAGE
+    exit
+fi
+
+# Logging helper function
+logit() {
+  echo "$(date -u) $1";
+}
+
+# Assert datalad exists
+assert_datalad_exists() {
+  command -v datalad &> /dev/null || { logit "ERROR Datalad could not be found!"; exit 1; }
+  logit "INFO Datalad found, proceeding to get data...";
+}
+
+# Assert antsRegistration exists
+assert_antsRegistration_exists() {
+  command -v antsRegistration &> /dev/null || { logit "ERROR antsRegistration could not be found!"; exit 1; }
+  logit "INFO antsRegistration found, proceeding...";
+}
+
+main() {
+
+    while getopts ":f:t:" opt; do
+        case $opt in
+            f)
+                src_path=$OPTARG
+                logit "DEBUG Source template path: ${src_path}"
+                ;;
+            t)
+                target_path=$OPTARG
+                logit "DEBUG Target template path: ${target_path}"
+                ;;
+            \?)
+                logit "ERROR Invalid option: -$OPTARG"
+                exit 1
+                ;;
+            :)
+                logit "ERROR Option -$OPTARG requires an argument"
+                exit 1
+                ;;
+        esac
+    done
+
+    assert_datalad_exists;
+    assert_antsRegistration_exists;
+
+    src_name=$(basename $(dirname $src_path));
+    IFS="-"; arr_src_name=($src_name); unset IFS;
+    target_name=$(basename $(dirname $target_path));
+    IFS="-"; arr_target_name=($target_name); unset IFS;
+    output_dir_prefix="${arr_src_name[1]}_to_${arr_target_name[1]}";
+    logit "DEBUG Output directory prefix: ${output_dir_prefix}";
+
+    # Resolve symlinks
+    full_src_path=$(realpath "$src_path");
+    logit "DEBUG Resolved source template path: ${full_src_path}";
+    full_target_path=$(realpath "$target_path");
+    logit "DEBUG Resolved target template_path: ${full_target_path}";
+
+    # Create output directory if not found and change directory
+    mkdir -p "xfms/${output_dir_prefix}";
+    cd "${PWD}/xfms/${output_dir_prefix}";
+
+    antsRegistration \
+        --verbose 1 \
+        --dimensionality 3 \
+        --float 0 \
+        --collapse-output-transforms 1 \
+        --output $output_dir_prefix \
+        --interpolation Linear \
+        --use-histogram-matching 0 \
+        --winsorize-image-intensities [ 0.005,0.995 ] \
+        --initial-moving-transform [ $full_src_path,$full_target_path,1 ] \
+        --transform Rigid[ 0.1 ] \
+        --metric MI[ $full_src_path,$full_target_path,1,32,Regular,0.25 ] \
+        --convergence [ 1000x500x250x0,1e-6,10 ] \
+        --shrink-factors 8x4x2x1 \
+        --smoothing-sigmas 3x2x1x0vox \
+        --transform Affine[ 0.1 ] \
+        --metric MI[ $full_src_path,$full_target_path,1,32,Regular,0.25 ] \
+        --convergence [ 1000x500x250x0,1e-6,10 ] \
+        --shrink-factors 8x4x2x1 \
+        --smoothing-sigmas 3x2x1x0vox \
+        --transform SyN[ 0.1,3,0 ] \
+        --metric MI[ $full_src_path,$full_target_path,1,32] \
+        --convergence [ 100x70x50x0,1e-6,10 ] \
+        --shrink-factors 8x4x2x1 \
+        --smoothing-sigmas 3x2x1x0vox \
+        --write-composite-transform 1
+
+    # Change to root
+    cd ../../;
+
+    logit "INFO Done. Data in ${PWD}/xfms/${output_dir_prefix}";
+}
+
+main "$@"