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Software Options

PCA on EEG/ERP data can be conducted using either regular statistics software (e.g. SPSS, SAS, R) or specialized software like the ERP PCA Toolkit. As we fill out the information on this page, checkout the overview on the blog.

Install ERP PCA Toolkit

  1. Grab the dependencies (EEGLab and FieldTrip)
  2. Unpack and place the toolboxes in a easy to access location (e.g. /Users/Shared)
    1. I suggest that you have one folder per toolbox (e.g. /Users/Shared/eeglab and /Users/Shared/fieldtrip)
    2. Remove the “slimmed down” FieldTrip install in EEGLab in eeglab/external
    3. Disable binary ICA in EEGLAB: modify ICABINARY line (~56) in eeglab/functions/sigprocfunc/icadefs.m to be ICABINARY=[ ];
  3. Add each toolbox to your path
    1. Add PCA Toolkit to your path including sub-folders
    2. Add EEGLab to your path without the subfolders
    3. Add FieldTrip to your path without the subfolders
      1. You'll need to then type ft_defaults on MATLAB prompt and then save the path again

Preparing Data for PCA

Whether you are conducting a PCA using software such as R or the ERP PCA Toolkit, the data preparation for most PCAs is roughly the same. You should conduct preprocessing in your software of choice. PCA Toolkit has routines for handing the preprocessing, but you could just as easily the software from your manufacturer (e.g. Net Station). In the end, your data should have gone through some set of the following:

  1. Filtering
  2. Segmentation
  3. Artifact Detection
  4. Baseline Correction
  5. Re-referencing (e.g. Average Reference)
  6. Averaging
eegerp/pca.txt · Last modified: 2014/06/23 11:40 by pmolfese