Table of functions

function

description

output

convert_to_BIDS()

Wrapper function for the whole workflow described below. Performs the setup of the ‘user_settings.R’ file, DICOM conversion,
reads the json sidecar files, starts the ‘sequence mapper’, copies the file into BIDS standard, creates a diagnostic dashboard and runs the ‘Shiny BIDS’ viewer.

All the outputs are described below.

select_user_settings_file()

Select a ‘user_settings.r’ file or create one with a point-and-click workflow.

The ‘user_settings.R’ file and the path to it.

prepare_environment()

Uses the input from the ‘user_settings.R’ file to create all environment variables and runs some checks on the data.

Creates environment variables and dataframes.

install_dcm2niix()

Downloads and unpacks ‘dcm2niix’ cite{Li2016} to the output folder.

Downloads dcm2niix to the output folder.

dcm2nii_converter_anon()

Converts the DICOM images to NIfTI and removes all sensitive information from the header and the json sidecar files.

NIfTI (anonymized header), json sidecar (anonymized)

dcm2nii_converter_json()

Extracts only the json sidecar files with the sensitive information from the DICOM images.

json sidecar

read_json_headers()

Reads all json sidecars, builds a dataframe containing all this information and saves it.

sequence_overview.tsv, json_metadata.tsv

sequence_mapper()

Starts the ‘sequence mapper’ shiny app to edit all unique sequence filenames to BIDS.

sequence_map.tsv

check_sequence_map()

Checks if all entries of the ‘sequence mapper’ were edited.

copy2BIDS()

Copies and renames the files from the temporary folder to a BIDS sourcedata folder. Creates other required BIDS files.

copy2BIDS.tsv, CHANGES, README, dataset_description.json, participants.json, participants.tsv

start_bids_validator()

Starts the BIDS-Validator in Docker (in Docker is installed) on the BIDS folder, otherwise the BIDS-Validator website is launched.

Diagnostic output in the terminal about the BIDS validity of the dataset.

run_shiny_BIDS()

Starts the ‘Shiny BIDS’ MR viewer app. This function can also be used on other datasets, when giving a BIDS path as argument.

delete_temp_nii_files()

Asks the user, if the temporary files should be deleted. Only recommended, when all data is converted and BIDS validity is ensured.