diff --git a/clpipe/cli.py b/clpipe/cli.py index d60f71da..b4e0f5dc 100644 --- a/clpipe/cli.py +++ b/clpipe/cli.py @@ -395,17 +395,21 @@ def glm_l2_preparefsf_cli(glm_config_file, l2_name, debug): help='Your GLM configuration file.') @click.option('-l1_feat_folders_path', type=CLICK_DIR_TYPE_EXISTS, default=None, required=False, - help='Location of your L1 FEAT folders.') -@click.option('-debug', is_flag=True, + help='Directory containing your L1 FEAT folders.') +@click.option('-remove_reg_standard', is_flag=True, default=False, + help='Remove reg_standard folders (generated by L2) in addition to reg.') +@click.option('-debug', is_flag=True, default=False, help='Flag to enable detailed error messages and traceback') def glm_apply_mumford_workaround_cli(glm_config_file, l1_feat_folders_path, - debug): + remove_reg_standard, debug): """ Apply the Mumford registration workaround to L1 FEAT folders. Applied by default in glm-l2-preparefsf. This command is useful for applying the Mumford workaround to single-run subjects who skip L2, allowing you to still combine them with multiple-run subjects at L3. + + Must provide GLM config file OR a path to your L1 FEAT folders. """ from .glm_l2 import glm_apply_mumford_workaround if not (glm_config_file or l1_feat_folders_path): @@ -413,7 +417,8 @@ def glm_apply_mumford_workaround_cli(glm_config_file, l1_feat_folders_path, "or '-l1_feat_folders_path' required.")) glm_apply_mumford_workaround( glm_config_file=glm_config_file, - l1_feat_folders_path=l1_feat_folders_path, debug=debug + l1_feat_folders_path=l1_feat_folders_path, debug=debug, + remove_reg_standard=remove_reg_standard )