Table of diagnostic files

filename	description	variables
dicom_paths.tsv	Output of the ‘prepare_environment()’ function. Shows the extracted dicom folders, input and output paths, and the applied regular expressions.	Take care, that your “subject/group/session_id” matches the regular expressions. Inspect the ‘output_path’ variables to find out, where the data will be saved after converting by dcm2niix cite{Li2016}. The ‘rest_string’ variables contain the removed information from the subject names.
json_metadata.tsv	Output of the ‘read_JSON_headers()’ function. The ‘create_dashboard()’ uses the information from this file.	Subject, group, session and sequence variables for identification and all physical MR parameters from the JSON sidecar.
sequence_overview.tsv	The ‘sequence_mapper()’ creates this file. It gives an overview of the number of images per unique sequence per session.	The ‘sequence’ column is the identifier column, ‘possible sequence’ is based on the regular expression from the ‘user_settings.R’ file. Per session one column is created containing the number of files. The ‘subject_session_merge’ column contains each subject with this sequence, up to a number of 30 observations.
sequence_map.tsv	The ‘sequence_mapper()’ creates and updates this file with each unique sequence ID from the ‘json_metadata.tsv’. Based on this file the ‘copy2BIDS’ output paths are created.	The variables show the total number of sequences with the unique ID; the sequence type is identified by the regular expression from the ‘user_settings.R’ file. ‘BIDS_sequence’ and ‘BIDS_type’ need to be manually matched with the sequence_mapper() to the BIDS specification. The ‘relevant’ column is used for sequence selection. It is coded with ‘0’ for “no export to BIDS” and ‘1’ for “copy this file into BIDS”.
copy2bids.tsv	Output of the copy2BIDS() function. Shows the input and output file paths of each file.	Variables per subject, session and sequence ID. Main information is in the ‘input_file_paths’ and ‘output_file_path’ columns.