This lesson is still being designed and assembled (Pre-Alpha version)

Initializing Data into BIDS

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I get my data into a BIDS compliant folder structure?

  • What does a BIDS folder structure look like?

Objectives
  • Understand how to initialize your data into BIDS.

Creating a BIDS folder structure

Initializing data into a BIDS compliant folder structure will result in individual subject folders that contain an eeg folder. All of the EEG files for that participant will be stored within sub-*/eeg/ folders.

To make the data compliant with BIDS, run the bids_face13.m script in the Matlab Command Window:

>> bids_face13

A file chooser window will pop up when running the bids_face13.m script. This file chooser is asking where you want the sub-*/eeg folders to be created. Select the project directory (Face13 folder) with the file chooser.

Creating the sub-*/eeg/ folders in the root of your project directory will create a folder structure that looks like this:

BIDS Folder Structure

Several files will be produced within each sub-*/eeg/ folder. All of the file names contain the subject number as well as the task name and a suffix to denote the information that is saved within that file. For example, the EEG recording data files have a suffix of _eeg and are saved as .edf files.

Once this procedure is completed, your initialized data will be in the BIDS standard (sub-*/eeg/) in the root of your project folder.

Exploring the formatted text files with the participant folders

Now that the data sessions are BIDS compliant many of the data parameters are available within formatted text files. This makes it easy to explore the session parameters using a folder browser and simple text editor. Note that this also makes it very efficient for tools and platform to access relevant session parameters without having to read the large data files.

BIDS EEG tsv

Digging down into the “BIDSification” process

The scripts used in this workshop use a forked version of the bids_matlab_tools EEGLAB plugin (https://github.com/sccn/bids-matlab-tools). We can explore the specifics of the process by examining the “bids_face13” script provided for this lesson.

>> edit bids_face13

Edit bids_face13

The bids_export function is the tool that does the BIDS compliant data writing of an EEGLAB EEG data structure. Looking through this function provides the information about what inputs are required to generate the BIDS compliant data set, as well as what options are available to modify the output.

>> edit bids_export

Edit bids_export

Key Points

  • Now the data are initialized into the BIDS standard