from PyNutil import PyNutil pnt = PyNutil(settings_file=r"PyNutil/test/test8_PyNutil_fixed.json") ##Use flat can be set to True if you want to use the flat file # instead of the visualign json (this is only useful for testing and will be removed) pnt.get_coordinates(object_cutoff=0, use_flat=True) pnt.quantify_coordinates() pnt.save_analysis("PyNutil/outputs/test8_PyNutil_bigcaudoputamen_newatlasmaps") # remove name, r, g, b, from pixel_ # add to region_areas df