What is in my ‘user_settings.R’ file?

You can also edit the file “user_settings.R” manually to your needs.

Variable	Example	Description
path_input_dicom	“/media/niklas/BIDS_data/dicom/”	Input path, where your DICOM folders are inside of session folders
path_output	“/media/niklas/BIDS_data/BIDSconvertR”	A path, where all the output of the converter should be written to.
study_name	“BiDirect Study”	Your study name, only needed for the dashboard rendering.
regex_subject_id	“[:digit:]{5}”	Regex defining your unique subject ID’s.
regex_group_id	“[:digit:]{1}(?=[:digit:]{4})”	Regex defining the group ID (if present).
regex_remove_pattern	“[:punct:]{1}|[:blank:]{1}|((b|d)i(d|b)i|bid|bd|bdi)(ect|rect)($|(rs|T2TSE|neu))”	These regex will be removed from the file names.
sessions_id_old	c(“Baseline”, “FollowUp”, “FollowUp2”, “FollowUp3”)	The folder (and session) names before conversion
sessions_id_new	c(“0”, “2”, “4”, “6”)	The folder (and session) names after conversion. These can be identical to “sessions_id_old”. But note, that in BIDS a number is the way to go.
mri_sequences	“T1|T2|DTI|fmr|rest|rs|func|FLAIR|smartbrain|survey|smart|ffe|tse”	These are regular expressions, which should be matched to your MRI sequence ID’s.
dcm2niix_argument_string	“-ba y -f %d -z y -w 0 -i y”	string of the arguments, which are used for dcm2niix, can be changed.

Table 1: Information in the user settings file