--- a
+++ b/adpkd_segmentation/process_nifti.py
@@ -0,0 +1,29 @@
+"""Process nifti annotations to png masks"""
+
+from argparse import ArgumentParser
+from pathlib import Path
+
+from adpkd_segmentation.utils.nifti_utils import process_nifti_dirs
+
+# "source" can be any nested directory structure containing study directories
+# each study directory should have a unique name, and it should
+# contain "DICOM_anon" dir containing dcm files and "Untitled.nii.gz"
+# check nifti_utils for expected constant definitions
+
+# all study dirs will be processed and copied to a single root target dir
+parser = ArgumentParser()
+parser.add_argument(
+    "source", type=str, help="Source directory with annotations"
+)
+parser.add_argument(
+    "target", type=str, help="Target directory for processed studies"
+)
+
+if __name__ == "__main__":
+    args = parser.parse_args()
+    source_dir = Path(args.source)
+    target_dir = Path(args.target)
+    print(
+        f"Processing studies: \nSource {source_dir},  Target {target_dir}\n\n"
+    )
+    process_nifti_dirs(source_dir, target_dir)