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Now that our model has been fit, we’d like to calculate some frequency-domain measures, such as the spectrum, coherence, and granger-causality. Bring up the Connectivity Estimation GUI by selecting the menu item Tools > SIFT > Connectivity. You can start this from the command line for a single dataset EEG using:

 EEG = pop_est_mvarConnectivity(EEG);

You should now see the GUI shown in the figure below. Here, we can compute all the measures (and more) listed in Table 4 in section 4.3. We can specify a list of frequencies at which to compute the measure(s), and we can do some simple conversions of complex measures and spectral densities.

For our example, let’s compute the direct DTF (with full causal normalization, denoted dDTF08), the complex coherence, the partial coherence, and the complex spectral density over the frequency range 2-50 Hz (with 1 Hz resolution). Your options should be set as the figure and table below:



Select connectivity measures

Direct DTF (with full causal norm.)
Complex Coherence (Coh)
Partial Coherence (pCoh)
Complex Spectral Density (S)

return squared amplitude of complex measures


convert spectral density to decibels


Frequencies (Hz)


Screen Shot 2023-08-25 at 5 02 27 PM

Figure caption. Connectivity estimation GUI generated by pop_est_mvarConnectivity(). Here, we have chosen to estimate the Direct DTF (with full causal normalization; dDTF08), the Complex Coherence (Coh), the Partial Coherence (pCoh), and the Spectral Density (S).

While selecting additional measures only marginally increases the computational time, doubling the number of measures will generally double the memory demands. Click OK to continue. You should now get a prompt notifying you of how much memory will be required (for each condition). If you have enough memory to continue, click OK. A progress bar will appear, showing the status of the connectivity estimation for each condition.

If you do not wish to use the GUI, the same may be achieved from the command line using:

EEG = pop_est_mvarConnectivity( EEG, 'nogui', 'ConnectivityMeasures', ...
             {'dDTF08' 'Coh' 'pCoh' 'S'}, 'Frequencies', [2:50], 'VerbosityLevel', 1);