| add_BIDS_metadata | This function adds all required BIDS metadata: 'CHANGES',... |
| add_participants_tsv | This function creates the required BIDS files... |
| check_BIDS_plausibility | Checks the plausibility of entered BIDS sequences based on... |
| check_BIDS_plausibility2 | Title |
| check_dataframe | Checks dataframe for plausibility |
| check_filenames | Checks the filenames |
| check_folder_order | Checks the folder order, reads the directory, extracts... |
| check_folder_order_df | Checks the folder order |
| check_sequence_map | Checks sequence map |
| cleaning_session_ids | Wrapper function for the editing of session-IDS |
| cleaning_subject_ids | Function to clean the input subject-ID's from redundant... |
| convert_to_BIDS | The core function, which converts the DICOM to NII, extracts... |
| copy2BIDS | Prepares and copies files to BIDS |
| copy_files | Copies files, if they don't exist in target |
| create_BIDS_regex | Creates the BIDS regular expression |
| create_dashboard | Creates the internal dashboard. This one contains sensitive... |
| create_environment_variables | Sets up the environment, creates needed variables variables |
| create_metadata | Creates template strings for BIDS |
| create_short_ids | Create short IDs |
| create_subject_session_df | Extracts the input data folder structure |
| create_taskname_metadata | Extracts the sequence id and RepetitionTime of functional... |
| create_user_settings | Creates a user setting template file at working directory or... |
| dcm2nii_converter | dcm2niix system calls using a list from dcm2nii_wrapper |
| dcm2nii_converter_anon | Converts the DICOM to anonymized NII and JSON files. |
| dcm2nii_converter_json | Converts the DICOM to only JSON files, that contain all... |
| dcm2nii_wrapper | Creates the dcm2niix system commands for the conversion |
| delete_temp_nii_files | Deletes temporary files |
| edit_session_df | Enables user edits to the session ID. |
| editTable | Sequence mapper shiny app. |
| get_json_headers | Extracts json headers from multiple files with different... |
| get_user_input | Start function for the user inputs, asks for input directory,... |
| install_dcm2niix | installs dcm2niix from Chris Rordens Github Repository, also... |
| list_dicom_folders | Finds dicom folders in dicom/session/subject folder structure |
| list_json_files | This function lists all json files in the folder. It extracts... |
| path_to_folder | Create folders from (list of) filenames |
| pipe | Pipe operator |
| prepare_environment | Prepares the environment with custom variables based on the... |
| print_passed_time | Prints progress of files in list of files |
| read_json_headers | Extracts the information from each json and merges it to the... |
| run_shiny_BIDS | Starts the BiDirect BIDS viewer |
| select_user_settings_file | Wrapper function to select and check the user input |
| sequence_mapper | The sequence mapper function (1) checks if there is already a... |
| start_bids_validator | Open BIDS validator in DOCKER |
| start_bids_validator_online | Open BIDS validator homepage |
| write_metadata_bids | This function writes a string to a path in UTF-8. |
