The installation procedure

Installing R and RStudio and downloading sample data:

To install the BIDSconvertR on Windows or Linux follow the instructions.
Download the BIDScoin example data : Download here. Please be aware that the data has been compressed twice using gunzip (suffix: ‘.gz’) and tar (suffix: ‘.tar’). You need to unpack both. Some programs do this in one step, others need to extract it twice. The data is fine, when you can easily click down the folder structure.

Table of contents

The installation procedure
The BIDSconvertR workflow

The BIDSconvertR workflow

This procedure should demonstrate how to use the BIDSconvertR. We appreciate the BIDScoin team’s permission to use their sample data. This tutorial only covers the basic steps. You can find a detailed description including visualizations in the “usage notes” section.

This workflow covers each stage of the BIDSconvertR workflow:

Launch RStudio and use the R console from here on.
Execute library("bidsconvertr", quietly = TRUE).
Use the convert_to_BIDS()command to launch the tool.

Creation of ‘user_settings.R’ file.

Create your own ‘user_settings.R’ file by following the popup messages.


*Screenshot of the dialog, that lets you select your user_settings file. Does only makes sense if you already created one!

Step 1: Choose the input folder that contains the DICOM’s (here ‘bidscointutorial\raw’).


Screenshot of the folder selection window,where you select the root folder, that contains all folders with dicoms. ‘../bidscointutorial/raw’

Step 2: Select the `../subject/session/..` order of folders.


Screenshot of the input data structure selection window. The BIDScoin data is structured into ‘subject/session’ folders

Step 3: Create and choose the output folder. All BIDSconvertR files (including the ‘user_settings.R’ file) are saved here.


Screenshot of the folder selection window for the output folder.

Step 4: Do not use the “subject-ID” or “pattern to remove” features. You have compliant subject-IDs!


Screenshot of the dialog box asking for the additional feature of subject-IDs editing with regular expressions.

GUI: sequence mapper

Use the sequence mapper to rename your files in accordance with BIDS, click “save” and close the window. The workflow should automatically launch the next steps.
A full documentation of the sequencemapper can be found here


Screenshot of the sequence mapper when entering the BIDS-compatible sequence-IDs.

Video demonstration

The video takes a few seconds to load.

Default values for tutorial data

Here you find the entries as text for copy & pasting. Alternatively, download the sequence_map.tsv from this link, right-click, save, and replace the file in your BIDS output folder.

sequence	BIDS_type	BIDS_sequence	relevant
t1_mprage_sag_ipat2_1p0iso	anat	T1w	1
AAHead_Scout_32ch-head	anat	smart	0
cmrr_2p4iso_mb8_TR0700	func	task-reward_acq-mp8_echo-1_bold	1
cmrr_2p4iso_mb8_TR0700_SBRef	func	task-reward_acq-mp8_echo-1_sbref	1
cmrr_2p5iso_mb3me3_TR1500_e1	func	task-stop_acq-mp3m3_run-1_bold	1
cmrr_2p5iso_mb3me3_TR1500_e2	func	task-stop_acq-mp3m3_run-2_bold	1
cmrr_2p5iso_mb3me3_TR1500_e3	func	task-stop_acq-mp3m3_run-3_bold	1
cmrr_2p5iso_mb3me3_TR1500_SBRef_e1	func	task-stop_acq-mp3m3_run-1_sbref	1
cmrr_2p5iso_mb3me3_TR1500_SBRef_e2	func	task-stop_acq-mp3m3_run-2_sbref	1
cmrr_2p5iso_mb3me3_TR1500_SBRef_e3	func	task-stop_acq-mp3m3_run-3_sbref	1
field_map_2p4iso_e1	fmap	acq-2p4_magnitude1	1
field_map_2p4iso_e2	fmap	acq-2p4_magnitude2	1
field_map_2p4iso_e2_ph	fmap	acq-2p4_phasediff	1
field_map_2p5iso_e1	fmap	acq-2p5_magnitude1	1
field_map_2p5iso_e2	fmap	acq-2p5_magnitude2	1
field_map_2p5iso_e2_ph	fmap	acq-2p5_phasediff	1

Now the data is automatically saved into BIDS, the BIDS validator is started, and the Shiny BIDS viewer starts.