This toolbox was designed as part of an independent study to facilitate batch processing of EEG datasets.

• Fieldtrip: https://www.fieldtriptoolbox.org/

  • Most functionality uses this toolbox and it is required.
  • Robert Oostenveld, Pascal Fries, Eric Maris, and Jan-Mathijs Schoffelen. FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data. Computational Intelligence and Neuroscience, 2011; 2011:156869. https://doi.org/10.1155/2011/156869

• mTRF: https://github.com/mickcrosse/mTRF-Toolbox

  • mTRF analysis uses this toolbox
  • Crosse, M. J., Di Liberto, G. M., Bednar, A., & Lalor, E. C. (2016). The multivariate temporal response function (mTRF) toolbox: a MATLAB toolbox for relating neural signals to continuous stimuli. Frontiers in human neuroscience, 10, 604. https://doi.org/10.3389/fnhum.2016.00604

• Use git or just download a zip of this toolbox and extract it somewhere on your hard drive.

• Add eeg_pipeline folder to Matlab's path

• In the command line, run: saeeg.BatchGUI

• A gui should appear.

• Use the Data Source button to locate the parent directory of your data.

• Use the Analysis Output button to locate where the analysis results should be written.

• The File Pattern fieldcan be used to restrict which files are found under the Data Source directory.

  • Recursively find all files: **/*
  • Recursively find 'bdf' files only: **/*.bdf
  • Recursively find all files that contain the string "PoolB": **/*PoolB*
  • Use more complex regular expressions to further restrict files.

• Select a folder or files individually in the file tree at the left.

• The dropdown box at the right-top of the gui should populate with analysis functions (really their own classes) that are compatible with the data type of selected files.

• Use the settings menu at the top of the gui to customize program behavior.

• A typical pipeline might look like:

  1. biosemi_preprocessing - convert biosemi data to fieldtrip data format for further processing
  2. data_concatenate - concatenate data based on simple file naming rules
  3. data_ica - compute independant component analysis. Results in comp component datatype
  4. comp_pregenerate_topomaps - pregenerate ica topographic maps and gui for speedy artifact selection and rejection
  5. fig_comp_mark_topomaps - runs the gui to select and reject ica artifacts
  6. data_mTRF - run forward or backward mTRF analysis (uses mTRF-Toolbox, see reference above)

• To add more functions, copy and modify an existing class under eeg_pipeline\+saeeg\+agui
• Each class requires a constructor that takes in MasterObj and parent.
  • MasterObj contains general program information and may or may not be useful
  • parent is a handle to the gui panel that can be used for user-modifiable parameters
• Each class also requires two additional functions: run_analysis and create_gui

• This function accepts the class object and a saeeg.FileQueue object (often simply coded as Q in existing classes)
• Analysis parameters are specified using the create_gui function (see below).
• The FileQueueobject handles the list of files that are selected and need to be processed.
• Use Q.CurrentFile to get the current full path and filename.
• Use Q.mark_completed to indicate that the current file has been processed.
• Use Q.start_next to kick off the next file in the queue if available.

• This function is used to setup a simple interface for specifying parameters.
• Use standard Matlab user interface objects, such as uieditfield, uitable, etc.
• Read the values of these fields in the run_analysis function to specify your analysis parameters.