diff --git a/chimera/chimera.py b/chimera/chimera.py index 4bc175a..0e20698 100644 --- a/chimera/chimera.py +++ b/chimera/chimera.py @@ -133,7 +133,7 @@ def __init__(self, parc_code, else: self.suprafolder = os.path.join(chim_dir, 'config', 'supraregions') - self.parc_dict, self.supra_dict = _load_parcellations_info(parc_json=parc_dict_file, supra_folder=supra_folder) + self.parc_dict, self.supra_dict = load_parcellations_info(parc_json=parc_dict_file, supra_folder=supra_folder) #### Filtering the parcellation dictionary according to the parcellation code #### supra_names = list(self.parc_dict.keys()) @@ -969,7 +969,7 @@ def build_parcellation(self, t1:str, bids_dir:str, aseg_parc.adjust_values() # Creating the parcellation for the extra regions - extra_parc = _create_extra_regions_parc(aparc=nii_image) + extra_parc = create_extra_regions_parc(aparc=nii_image) # Remove the nifti file os.remove(nii_image) @@ -1736,7 +1736,7 @@ def build_parcellation(self, t1:str, bids_dir:str, del chim_parc # Loading the JSON file containing the available parcellations -def pipeline_info(pipe_json:str=None): +def _pipeline_info(pipe_json:str=None): """ Load the JSON file containing the pipeline configuration. @@ -1766,7 +1766,7 @@ def pipeline_info(pipe_json:str=None): return pipe_dict -def set_templateflow_home(tflow_home: str='local'): +def _set_templateflow_home(tflow_home: str='local'): """ Setting up the templateflow home directory. @@ -1805,7 +1805,7 @@ def set_templateflow_home(tflow_home: str='local'): return updated_tflow_home -def mix_side_prop(st_dict: dict, boolsort: bool = True): +def _mix_side_prop(st_dict: dict, boolsort: bool = True): """ Method to mix all the properties for a specific supra-region and a specific method. @@ -2040,7 +2040,7 @@ def create_extra_regions_parc(aparc:str, offset:int=5000): return rh_tmp_parc -def build_args_parser(): +def _build_args_parser(): formatter = lambda prog: argparse.HelpFormatter(prog, max_help_position=52) @@ -2253,7 +2253,7 @@ def build_args_parser(): parcodes = args.parcodes[0].split(sep=',') - parc_dict, supra_dict = _load_parcellations_info() + parc_dict, supra_dict = load_parcellations_info() supra_reg_names = list(parc_dict.keys()) n_supra = len(supra_reg_names) @@ -2339,7 +2339,7 @@ def print_availab_parcels(reg_name=None): """ - data, supra_dict = _load_parcellations_info() + data, supra_dict = load_parcellations_info() if reg_name is None: supra_keys = data.keys() diff --git a/chimera/config/supraregions/Cerebellum.tsv b/chimera/config/supraregions/Cerebellum.tsv index 9f5d295..03a8263 100644 --- a/chimera/config/supraregions/Cerebellum.tsv +++ b/chimera/config/supraregions/Cerebellum.tsv @@ -1,31 +1,37 @@ supraregion method hemi index name color Cerebellum F lh 8 cer-lh-cerebellum #e69422 Cerebellum F rh 47 cer-rh-cerebellum #e69422 -Cerebellum R lh 1 cer-lh-i_iv #049494 -Cerebellum R rh 2 cer-rh-i_iv #049494 -Cerebellum R lh 3 cer-lh-v #fabe77 -Cerebellum R rh 4 cer-rh-v #fabe77 -Cerebellum R lh 5 cer-lh-vi #a018ce -Cerebellum R mid 6 cer-mid-vermis_vi #ff5733 -Cerebellum R rh 7 cer-rh-vi #a018ce -Cerebellum R lh 8 cer-lh-crus_i #34a853 -Cerebellum R mid 9 cer-mid-vermis_crus_i #33ff57 -Cerebellum R rh 10 cer-rh-crus_i #34a853 -Cerebellum R lh 11 cer-lh-crus_ii #dfe6fc -Cerebellum R mid 12 cer-mid-vermis_crus_ii #5733ff -Cerebellum R rh 13 cer-rh-crus_ii #dfe6fc -Cerebellum R lh 14 cer-lh-viib #16394f -Cerebellum R mid 15 cer-mid-vermis_viib #a3e635 -Cerebellum R rh 16 cer-rh-viib #16394f -Cerebellum R lh 17 cer-lh-viiia #c3f7e4 -Cerebellum R mid 18 cer-mid-vermis_viiia #a1ff33 -Cerebellum R rh 19 cer-rh-viiia #c3f7e4 -Cerebellum R lh 20 cer-lh-viiib #ffd9b3 -Cerebellum R mid 21 cer-mid-vermis_viiia #ffa533 -Cerebellum R rh 22 cer-rh-viiib #ffd9b3 -Cerebellum R lh 23 cer-lh-ix #ff33a1 -Cerebellum R mid 24 cer-mid-vermis_ix #a3e635 -Cerebellum R rh 25 cer-rh-ix #ff33a1 -Cerebellum R lh 26 cer-lh-x #ffbe0b -Cerebellum R mid 27 cer-mid-vermis_x #9a031e -Cerebellum R rh 28 cer-rh-x #ffbe0b +Cerebellum S lh 1 cer-lh-i_iv #049494 +Cerebellum S rh 2 cer-rh-i_iv #049494 +Cerebellum S lh 3 cer-lh-v #fabe77 +Cerebellum S rh 4 cer-rh-v #fabe77 +Cerebellum S lh 5 cer-lh-vi #a018ce +Cerebellum S mid 6 cer-mid-vermis_vi #ff5733 +Cerebellum S rh 7 cer-rh-vi #a018ce +Cerebellum S lh 8 cer-lh-crus_i #34a853 +Cerebellum S mid 9 cer-mid-vermis_crus_i #33ff57 +Cerebellum S rh 10 cer-rh-crus_i #34a853 +Cerebellum S lh 11 cer-lh-crus_ii #dfe6fc +Cerebellum S mid 12 cer-mid-vermis_crus_ii #5733ff +Cerebellum S rh 13 cer-rh-crus_ii #dfe6fc +Cerebellum S lh 14 cer-lh-viib #16394f +Cerebellum S mid 15 cer-mid-vermis_viib #a3e635 +Cerebellum S rh 16 cer-rh-viib #16394f +Cerebellum S lh 17 cer-lh-viiia #c3f7e4 +Cerebellum S mid 18 cer-mid-vermis_viiia #a1ff33 +Cerebellum S rh 19 cer-rh-viiia #c3f7e4 +Cerebellum S lh 20 cer-lh-viiib #ffd9b3 +Cerebellum S mid 21 cer-mid-vermis_viiia #ffa533 +Cerebellum S rh 22 cer-rh-viiib #ffd9b3 +Cerebellum S lh 23 cer-lh-ix #ff33a1 +Cerebellum S mid 24 cer-mid-vermis_ix #a3e635 +Cerebellum S rh 25 cer-rh-ix #ff33a1 +Cerebellum S lh 26 cer-lh-x #ffbe0b +Cerebellum S mid 27 cer-mid-vermis_x #9a031e +Cerebellum S rh 28 cer-rh-x #ffbe0b +Cerebellum S lh 29 cer-lh-dentate #4c4c4c +Cerebellum S rh 30 cer-rh-dentate #4c4c4c +Cerebellum S lh 31 cer-lh-interposed #7f7f7f +Cerebellum S rh 32 cer-rh-interposed #7f7f7f +Cerebellum S lh 33 cer-lh-fastigial #b2b2b2 +Cerebellum S rh 34 cer-rh-fastigial #b2b2b2