input_level_fname = None input_ref_gm_seg = None compute_ratio = False if seg_param.debug: print '\n*** WARNING: DEBUG MODE ON ***\n' fname_input = model_param.path_model + "/errsm_34.nii.gz" fname_input = model_param.path_model + "/errsm_34_seg_in.nii.gz" else: parser = get_parser() arguments = parser.parse(sys.argv[1:]) input_target_fname = arguments["-i"] input_sc_seg_fname = arguments["-s"] if "-model" in arguments: model_param.path_model = arguments["-model"] model_param.todo_model = 'load' 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"]