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, |
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. |