GETTING STARTED

In this first section you’ll see how to open the EEG Processor application, how to setup a new dataset, and how to open an existing dataset.

Video chapters

0:00 Download the EEG Processor

1:11 Start the EEG Processor

2:42 The interface

5:00 Create new dataset

Open the EEG Processor application

  • Navigate to the location of the ‘EEG_Processor.mlapp’ file and make sure to open it with Matlab 2021a or later.

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  • If you run the EEG Processor on the Woolcock Super-Computer, then the dependencies of EEGLAB and Fieldtrip will be automatically added.

    • Otherwise, you’ll have to specify where EEGLAB and Fieldtrip are located on your computer. The following dialogs will show. Press “Browse” and navigate to the folder that contains ‘eeglab.m’ and ‘ft_defaults.m’ respectively.

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The EEG Processor interface

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Top panel

Dataset path. Shows the path to the currently loaded dataset. Use the “Browse” button to select the BIDS dataset root directory, i.e. the location that contains the rawdata folder.

middle left panel

Files tabs. Shows a tree of subjects and associated files stored in the rawdata, the derivatives and the derivatives/*-first-level folders. Use the “Add subject” button to create a new subject, the “Collapse/Expand” button to collapse or expand the files-tree, the “Select/Deselect” button to select or deselect all shown files, and the “Filter” input field to filter files based on an expression, e.g. task_psg will only show files that contain that expression in the filename.

middle right panel

Properties tabs. Shows the properties of the dataset description, the selected subject and the selected files. See below for more info. TODO: add link

Bottom panels

Apply process to selected files. Use the dropdown menu to select a process, e.g. “Power Spectral Analysis” and then the “Add process” button to add the selected process for each selected file to the processes queue. Processes. Lists all processes in the queue. Use the “Up” and “Down” buttons to rearrange processes, the “Delete” button to remove processes, or the “Run” button to start the processes.

Creating a new BIDS dataset

  • Use the “Browse” botton in the dataset path panel to select the folder where you want to create a new BIDS dataset.

    • If the selected folder does not contain a dataset_description.json file, nor does it contain a rawdata folder with such a JSON file in it, then it will ask if you want to create a new dataset or not. Select “Yes, create a new dataset”

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  • The BIDS dataset contains 3 main folders,

    • the sourcedata folder contains data before harmonization, reconstruction, and/or file format conversion,

    • the rawdata folder contains unprocessed or minimally processed data, e.g. file format conversion,

    • the derivatives folder contains processed data and analysis output files.

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  • The rawdata folder contains the main dataset_description.json file. This plain text file is a tree-structered list of properties of the dataset. These properties can be changed via the EEG Processor application.

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Set the BIDS dataset properties

Simply use the input fields to change any of the dataset properties.

Note

The Sessions and Tasks panel are used for when you want to import a new file or select part of an existing file. Which will be discussed later. TODO: show link

Dataset name

Name of your dataset or project.

Dataset DOI

Full DOI link to the online repository of your dataset.

Dataset License

License for use of your open-source dataset by others.

Generated by

A name and description of who or what has created this dataset.

Authors

Your name and others who worked on the project.

Funding

Names of funding bodies and grant application IDs.

Ethics

Name of the institute and ethics committee(s) that granted permission to perform the project.

How to acknowledge

Short description of how others can acknowledge the use of your dataset, e.g. a publication.

Acknowledgments

List of publications or documents that were used as prior knowledge in your project.