seg_param.output_path = sct.slash_at_the_end(arguments["-ofolder"], slash=1) if "-t2" in arguments: input_t2_data = arguments["-t2"] if "-vert" in arguments: input_level_fname = arguments["-vert"] if "-use-levels" in arguments: model_param.use_levels = bool(int(arguments["-use-levels"])) if "-weight" in arguments: model_param.weight_gamma = arguments["-weight"] if "-denoising" in arguments: seg_param.target_denoising = bool(int(arguments["-denoising"])) if "-normalize" in arguments: seg_param.target_normalization = bool(int(arguments["-normalize"])) if "-means" in arguments: seg_param.target_means = arguments["-means"] if "-ratio" in arguments: if arguments["-ratio"] == '0': compute_ratio = False else: compute_ratio = arguments["-ratio"] if "-ratio-level" in arguments: if arguments["-ratio-level"] == '0': compute_ratio = False else: if ':' in arguments["-ratio-level"]: compute_ratio = arguments["-ratio-level"] else: sct.printv('WARNING: -ratio-level function should be used with a range of vertebral levels (for ex: "C2:C5"). Ignoring option.', 1, 'warning') if "-res-type" in arguments: seg_param.res_type = arguments["-res-type"]