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jessicasamogin edited this page Oct 18, 2023 · 8 revisions
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:: USER GUIDE ::

NET is an open-source MATLAB software for large-scale analysis of high-density electroencephalographic (hdEEG) data, from raw signals to activity and/or connectivity values.

Software requirements

NET requires MATLAB 2016b (MathWorks, download here) or later versions.

Installation

You can download the latest version of NET from Github (here).

** !! NOTE: download the folders stored here and save them in the net repository. A test dataset can be found at the same link **

Initialization

There are two option to run NET:

  • through the graphical-user interface (GUI) > open MATLAB and run net_start_gui.m
  • through the main script > open MATLAB and run net_start_no_gui.m

You don't need to add NET to the path, the software will do it automatically.

Use NET with the GUI

gui
  1. choose the processing directory, where NET will save the output of the analyses
  2. add the raw EEG, MRI and electrode positions files with the Load Datasets button
  3. set the preprocessing parameters (conversion, head model, signal processing and source localization) with the View/Edit Prepro Parameters button
  4. choose how to run the pipeline:
    • Sample Dataset > one step at a time on the chosen dataset
    • All Datasets > one step on all datasets together
    • All Datasets & Steps > each dataset is fully processed before automatically proceeding to the next one

The outputs at individual and/or group level can be visualized through the visualization pane at the bottom.

NOTES:

  • NET automatically copies two excel files in the processing folder: *_dataset.xlsx (list of input filenames) and *_parameters_prepro.xls (preprocessing parameters)
  • to perform activity, connectivity and statistical analysis, select Load Analysis Parameters and choose the template_parameters_analysis.xlsx file from the net/template_files folder. NET will copy it in the processing directory (*_parameters_analysis.xls)
  • for every dataset, NET creates a subdirectory containing three folders:
    • eeg_signal > processed channel data, ERP and ERS/ERD results at channel level
    • eeg_source > source reconstructed EEG data, ERP and ERS/ERD results at cortical level and connectivity results
    • mr_data > all the files related to the head model

Use NET with the main script

  1. copy the template_dataset.xlsx, template_parameters_prepro.xlsx and template_parameters_analysis.xlsx files from net/template_files folder to net/net_results
  2. fill in the Excel files with the information about the datasets and set to "on" or "off" the steps that you want to execute
  3. run net_start_no_gui.m

NOTES:

  • for every dataset, NET creates a subdirectory containing three folders:
    • eeg_signal > processed channel data, ERP and ERS/ERD results at channel level
    • eeg_source > source reconstructed EEG data, ERP and ERS/ERD results at cortical level and connectivity results
    • mr_data > all the files related to the head model
  • it is possible to visualize the results of the process with the GUI:
    1. run net_start_gui.m
    2. select net_results as processing directory
    3. from the Visualizations pane, choose which dataset/group results to visualize
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