def read_cmd_args(argv): import argparse parser = argparse.ArgumentParser(description='MMVT freeview preprocessing') parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_aseg_file', help='overwrite_aseg_file', required=False, default=0, type=au.is_true) parser.add_argument('--create_volume_file', help='create_volume_file', required=False, default=1, type=au.is_true) parser.add_argument('--electrodes_pos_fname', help='electrodes_pos_fname', required=False, default='') parser.add_argument('--way_points', help='way_points', required=False, default=0, type=au.is_true) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']} # print(args) return args
def read_cmd_args(argv=None): import argparse parser = argparse.ArgumentParser(description='MMVT template preprocessing') parser.add_argument('--flag', help='', required=False, default='') pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) return args
def read_cmd_args(argv=None): import argparse from src.utils import args_utils as au parser = argparse.ArgumentParser(description='MMVT stim preprocessing') parser.add_argument('-c', '--conditions', help='conditions names', required=False, default='contrast', type=au.str_arr_type) parser.add_argument('--mat_fname', help='matlab connection file name', required=False, default='') parser.add_argument('--mat_field', help='matlab connection field name', required=False, default='') parser.add_argument('--labels_exclude', help='rois to exclude', required=False, default='unknown,corpuscallosum', type=au.str_arr_type) parser.add_argument('--bipolar', help='', required=False, default=0, type=au.is_true) parser.add_argument('--norm_by_percentile', help='', required=False, default=1, type=au.is_true) parser.add_argument('--norm_percs', help='', required=False, default='1,99', type=au.int_arr_type) parser.add_argument('--stat', help='', required=False, default=STAT_DIFF, type=int) parser.add_argument('--windows', help='', required=False, default=0, type=int) parser.add_argument('--t_max', help='', required=False, default=0, type=int) parser.add_argument('--threshold_percentile', help='', required=False, default=0, type=int) parser.add_argument('--threshold', help='', required=False, default=0, type=float) parser.add_argument('--color_map', help='', required=False, default='jet') parser.add_argument('--symetric_colors', help='', required=False, default=1, type=au.is_true) parser.add_argument('--data_max', help='', required=False, default=0, type=float) parser.add_argument('--data_min', help='', required=False, default=0, type=float) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) if len(args.conditions) == 1: args.stat = STAT_AVG print(args) return args
def read_cmd_args(argv=None): import argparse parser = argparse.ArgumentParser(description='MMVT anatomy preprocessing') parser.add_argument('--template_subject', help='template subject', required=False, default='fsaverage') parser.add_argument('--surf_name', help='surf_name', required=False, default='pial') parser.add_argument('--cerebellum_segmentation_loose', help='', required=False, default=1, type=au.is_true) parser.add_argument('--overwrite', help='overwrite', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_subcorticals', help='overwrite', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_annotation', help='overwrite_annotation', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_morphing_labels', help='overwrite_morphing_labels', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_hemis_srf', help='overwrite_hemis_srf', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_labels_ply_files', help='overwrite_labels_ply_files', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_faces_verts', help='overwrite_faces_verts', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_ply_files', help='overwrite_ply_files', required=False, default=0, type=au.is_true) parser.add_argument('--solve_labels_collisions', help='solve_labels_collisions', required=False, default=0, type=au.is_true) parser.add_argument('--morph_labels_from_fsaverage', help='morph_labels_from_fsaverage', required=False, default=1, type=au.is_true) parser.add_argument('--fs_labels_fol', help='fs_labels_fol', required=False, default='') pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) args.necessary_files = {'mri': ['aseg.mgz', 'norm.mgz', 'ribbon.mgz', 'T1.mgz', 'orig.mgz'], 'surf': ['rh.pial', 'lh.pial', 'rh.inflated', 'lh.inflated', 'lh.curv', 'rh.curv', 'rh.sphere.reg', 'lh.sphere.reg', 'lh.white', 'rh.white', 'rh.smoothwm','lh.smoothwm'], 'mri:transforms' : ['talairach.xfm']} if args.overwrite: args.overwrite_annotation = True args.overwrite_morphing_labels = True args.overwrite_hemis_srf = True args.overwrite_labels_ply_files = True args.overwrite_faces_verts = True args.overwrite_fs_files = True print(args) return args
def read_cmd_args(argv=None): import argparse from src.utils import args_utils as au parser = argparse.ArgumentParser(description='MMVT template preprocessing') pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser)) print(args) return args
def read_cmd_args(argv=None): import argparse from src.utils import args_utils as au parser = argparse.ArgumentParser(description='MMVT template preprocessing') pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser)) # print(args) return args
def read_cmd_args(argv): import argparse from src.utils import args_utils as au parser = argparse.ArgumentParser(description='MMVT freeview preprocessing') parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true) parser.add_argument('--overwrite_aseg_file', help='overwrite_aseg_file', required=False, default=0, type=au.is_true) parser.add_argument('--create_volume_file', help='create_volume_file', required=False, default=1, type=au.is_true) parser.add_argument('--electrodes_pos_fname', help='electrodes_pos_fname', required=False, default='') parser.add_argument('--way_points', help='way_points', required=False, default=0, type=au.is_true) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']} print(args) return args
def read_cmd_args(argv=None): import argparse from src.utils import args_utils as au parser = argparse.ArgumentParser(description='MMVT stim preprocessing') parser.add_argument('--stim_channel', help='stim channel', required=True) parser.add_argument('--colors_map', help='activity colors map', required=False, default='OrRd') parser.add_argument('--norm_percs', help='normalization percerntiles', required=False, type=au.int_arr_type, default='1,95') parser.add_argument('--downsample', help='downsample', required=False, type=int, default=1) parser.add_argument('--file_frefix', help='file_frefix', required=False, default='psd_') parser.add_argument('--error_radius', help='error_radius', required=False, default=3, type=int) parser.add_argument('--elec_length', help='elec_length', required=False, default=4, type=int) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser)) print(args) return args
def read_cmd_args(argv=None): from src.utils import args_utils as au import argparse parser = argparse.ArgumentParser(description='MMVT electrodes preprocessing') parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true) parser.add_argument('--good_channels', help='good channels', required=False, default='', type=au.str_arr_type) parser.add_argument('--bad_channels', help='bad channels', required=False, default='', type=au.str_arr_type) parser.add_argument('--from_t', help='from_t', required=False, default='0', type=au.float_arr_type)# float) # was -500 parser.add_argument('--to_t', help='to_t', required=False, default='0', type=au.float_arr_type) # was 2000 parser.add_argument('--from_t_ind', help='from_t_ind', required=False, default=0, type=int) # was -500 parser.add_argument('--to_t_ind', help='to_t_ind', required=False, default=-1, type=int) # was 2000 parser.add_argument('--indices_shift', help='indices_shift', required=False, default=0, type=int) # was 1000 parser.add_argument('--conditions', help='conditions', required=False, default='') parser.add_argument('--raw_fname', help='raw fname', required=False, default='no_raw_fname_given') parser.add_argument('--ref_elec', help='referece electrode', required=False, default='') parser.add_argument('--stat', help='stat', required=False, default=STAT_DIFF, type=int) parser.add_argument('--electrodes_names_field', help='electrodes_names_field', required=False, default='names') parser.add_argument('--moving_average_window_size', help='', required=False, default=0, type=int) parser.add_argument('--field_cond_template', help='', required=False, default='{}') parser.add_argument('--input_type', help='', required=False, default='ERP') parser.add_argument('--input_matlab_fname', help='', required=False, default='') parser.add_argument('--start_time', help='', required=False, default='') parser.add_argument('--seizure_time', help='', required=False, default='') parser.add_argument('--window_length', help='', required=False, default=0, type=float) parser.add_argument('--seizure_onset_time', help='', required=False, default=0, type=float) parser.add_argument('--baseline_delta', help='', required=False, default=0, type=float) parser.add_argument('--time_format', help='', required=False, default='%H:%M:%S') parser.add_argument('--electrodes_groups_coloring_fname', help='', required=False, default='electrodes_groups_coloring.csv') parser.add_argument('--ras_xls_sheet_name', help='ras_xls_sheet_name', required=False, default='') parser.add_argument('--do_plot', help='do plot', required=False, default=0, type=au.is_true) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) args.ignore_missing = True for field in ['from_t', 'to_t']: if len(args[field]) == 1: args[field] = args[field][0] args.necessary_files = {'electrodes': ['{subject}_RAS.csv']} print(args) return args
def read_cmd_args(argv=None): import argparse parser = argparse.ArgumentParser(description='MMVT CT preprocessing') parser.add_argument('--ct_raw_input_fol', help='', required=False, default='') parser.add_argument('--ct_fol', help='', required=False, default='') parser.add_argument('--ct_org_name', help='', required=False, default='ct_org.mgz') parser.add_argument('--nnv_ct_name', help='', required=False, default='ct_no_large_negative_values.mgz') parser.add_argument('--register_ct_name', help='', required=False, default='ct_reg_to_mr.mgz') parser.add_argument('--negative_threshold', help='', required=False, default=-200, type=int) parser.add_argument('--no_negatives', help='', required=False, default=True, type=au.is_true) parser.add_argument('--register_cost_function', help='', required=False, default='nmi') parser.add_argument('--ct_threshold', help='', required=False, type=float, default=2000) parser.add_argument('--overwrite', help='', required=False, default=0, type=au.is_true) parser.add_argument('--print_only', help='', required=False, default=False, type=au.is_true) parser.add_argument('--ask_before', help='', required=False, default=False, type=au.is_true) parser.add_argument('--debug', help='', required=False, default=False, type=au.is_true) # find_electrodes: parser.add_argument('--n_components', help='', required=False, default=0, type=int) parser.add_argument('--n_groups', help='', required=False, default=0, type=int) parser.add_argument('--brain_mask_fname', help='', required=False, default='') parser.add_argument('--output_fol', help='', required=False, default=None, type=au.str_or_none) parser.add_argument('--clustering_method', help='', required=False, default='knn') parser.add_argument('--max_iters', help='', required=False, default=5, type=int) parser.add_argument('--cylinder_error_radius', help='', required=False, default=3, type=float) parser.add_argument('--min_elcs_for_lead', help='', required=False, default=4, type=int) parser.add_argument('--max_dist_between_electrodes', help='', required=False, default=20, type=float) parser.add_argument('--min_cylinders_ang', help='', required=False, default=0.1, type=float) parser.add_argument('--ct_thresholds', help='', required=False, default='99,99.9,99.95,99.99,99.995,99.999', type=au.float_arr_type) parser.add_argument('--min_joined_items_num', help='', required=False, default=1, type=int) parser.add_argument('--min_distance_beteen_electrodes', help='', required=False, default=2, type=float) # Dell parser.add_argument('--voxels', help='', required=False, default='', type=au.list_of_int_lists_type) parser.add_argument('--voxel', help='', required=False, default='', type=au.int_arr_type) # 102,99,131 parser.add_argument('--pixels_around_voxel', help='', required=False, default=30, type=int) parser.add_argument('--interactive', help='', required=False, default=0, type=au.is_true) parser.add_argument('--electrodes_names', help='', required=False, default='', type=au.str_arr_type) parser.add_argument('--group_name', help='', required=False, default='') parser.add_argument('--elc_name', help='', required=False, default='') parser.add_argument('--fig_name', help='', required=False, default='') parser.add_argument('--isotropization_type', help='', required=False, default=1, type=int) pu.add_common_args(parser) args = utils.Bag(au.parse_parser(parser, argv)) pu.set_default_folders(args) args.necessary_files = {'mri': ['brain.mgz']} global SUBJECTS_DIR, MMVT_DIR SUBJECTS_DIR = args.mri_dir MMVT_DIR = args.mmvt_dir print('Subjects dir: {}'.format(SUBJECTS_DIR)) print('MMVT dir: {}'.format(MMVT_DIR)) return args