This is surprising that you only ended with a UserWarning and not an exception. SimpleITK images are not compatible with skimage’s expectation of numpy arrays. You can get a numpy array from a SimpleITK image using the GetArrayFromImage method. I would suggest that you familiarize yourself with SimpleITK by going over the SimpleITK Jupyter notebooks. You can either clone the comprehensive repository or a shorter tutorial given at ISBI’18.