diff --git a/brainles_preprocessing/cli.py b/brainles_preprocessing/cli.py index 5490d51..465075a 100644 --- a/brainles_preprocessing/cli.py +++ b/brainles_preprocessing/cli.py @@ -59,11 +59,15 @@ def main( ), ], output_dir: Annotated[ - str | Path, + Path, typer.Option( "-o", "--output_dir", help="The path to the output directory", + exists=False, + file_okay=False, + dir_okay=True, + resolve_path=True, ), ], input_atlas: Annotated[ @@ -89,7 +93,6 @@ def main( Preprocess the input images according to the BraTS protocol. """ - output_dir = Path(output_dir) output_dir.mkdir(parents=True, exist_ok=True) # specify a normalizer