What is PACT?
PACT is a plug-in for EEGLAB. PACT stands for (cross-frequency) Phase-Amplitude Coupling Toolbox. See the github repository at https://github.com/sccn/PACT to submit bug reports or modify the codebase.
What data does PACT take?
Currently it takes continuous data only. PACT was originally developed for electrocorticographic (ECoG) data analysis.
What does PACT do?
In preparatory exploration, you may run a brute-force computation of PAC for all combinations of low-frequency oscillation (LFO) and highest-amplitude sampling (HAS) center frequencies. This computation may take a long time depending on the frequency resolution and bandwidth you specify. To compute each PAC value for a channel frequency-by-frequency combination, PACT performs the following steps:
1. Band-pass filter the data to extract HFO and LFO signals.
2. Hilbert transform the HFO signal to extract a time series of instantaneous amplitudes.
3. Hilbert transform the LFO signal to extract a time series of instantaneous phases.
4. (Highest-Amplitude Sampling, HAS): apply a threshold to select the N% highest HFO amplitudes. Obtain the HAS index from this.
5. For LFO phase, apply HAS index.
6. Combine HAS-indexed HFO and LFO indices into complex-valued phasors.
7. Compute the Modulation Index (Canotly et al., 2006) for the collection of HAS phasors constructed above.
8. Generate a collection of surrogate data by circularly permuting the phase time-series relative to the amplitude series.
9. Compute a surrogate set of Modulation Indices for which the null hypothesis should hold and determine a statistical threshold from their distribution.
10. Perform multiple comparison corrections based on the number of channels for which you are estimating PAC significance.
Note: To compute and perform statistics on the Mean Resultant Vector Length, PACT uses CircStat (Berens, 2009). To compute phase-sorted amplitude statistics, PACT uses K-S and Chi-square tests.
What do the PACT GUIs look like?
When successfully installed, the item 'PACT' should appear under 'Tools' (Figure 1). Currently it has 12 menus.
- Compute PAC: This launches the main GUI (Figure 2). When press ok, computation starts. When it done, statistics set up window pops up (described later).
- Phase freq range [lohz hihz]
- Amp freq range [lohz hihz]
- Highest amplitude sampling rate [%]
- Sampling pool: This is for the experimental purpose. Always choose 'Each channel'.
- If handpicked, event type and win size [+/- ms]: If you want to run the analysis using the data around event markers generated by either VidEd or MoBILAB, use this.
- Significance threshold [p]
- Number of surrogation [N]: This determines how many data points you want to generate surrogate data that represents for distribution of null hypothesis.
- Number of phase bins [N]: This affects sensitivity of circular statistics. Don't use too extremely large value (e.g. >100).
- Plot HFO-marked Raw data: This plot looks like Figure 3.
- Invert polarity: This is to invert EEG polarity by simply multiplying -1 to all the data.
- Handpick HFO(VisEd): This plot looks like Figure 4 left. You can choose the marking point by mouse click. For detailed explanation how to use this VisEd, see VisEd help.
- Handpick HFO(Mobilab): This plot looks like Figure 4 left. Similarly, you can choose the marking point by mouse click. Use whichever suit you.
- Copy event markers: This is to copy event markers from dataset 1 to dataset 2.
- Set up statistics: This shows a GUI that look like Figure 5.
- Plot Modulation Index: This shows a plot that look like Figure 7/8 top right.
- Plot Angular hist (bar)
- Plot Angular hist (polar): This shows a plot that look like Figure 7/8 bottom left.
- Plot phase-sorted amp: This shows a plot that look like Figure 7/8 bottom left. Each bar represents mean amplitude of each phase bin.
- Scan LFO freqs (very slow!): This pops up GUI like Figure 6. Start with N = 10 or around, and HAS rate of 0.3-10. Color normalization should be used when plotting Mean Resultant Vector Length.
What plots does PACT output?
1. LFO-HAS parameter space scan results (combination of LFO phase frequencies and HAS rates; the measure used may be either Mean Resultant Vector Length or Modulation Index.
2. Using Modulation Index with a confidence interval of 95% or 99%.
3a. Angular histogram displayed in a polar plot using Mean Resultant Vector Length.
3b. Angular histogram in a rectangular plot with phase unwrapped on the x-axis.
4. Bar graphs of LFO phase-sorted HFO-amplitudes.
Note that the number of phase bins in Figures 3a and 3b is determined by user input and affects the results of the circular statistics.
How PACT can be used, and how its output can be interpreted: A demo example
These plots show examples in which PACT was applied to electrocorticographic data for which a neurologist judged the channel( Ch) 1 signal to be pathological and the Ch2 signal to be normal.
First, exploratory LFO frequency scans were performed (Figures 7 and 8, top left; they are the same). We needed to run PACT several times, adjusting parameters; the result that showed the difference most clearly is plotted here. Mean Resultant Vector Length was chosen as the dependent variable, since it is naturally normalized from 0 to 1 and is therefore convenient for comparisons across channels. This plot shows two noticeable clusters of interest that showed differences between Ch1 and Ch2:.One is (LFO 0.5 Hz, HAS 3%,) the other (LFO 1.5 Hz, HAS 1.5%). We decided to run analysis for both combinations of parameters. Statistical significance level was set to 1% with Bonferroni-Holm correction (Note: here, since we have only 2 items to compare, B-H is the same as Bonferroni).
Caution and Limitation
The 'Handpick HFO' menu does not work with newer Matlab versions, which no longer support the graphics.cursorbar object. To use this function, use Matlab 2013 or older as a workaround.
Scanning Phase-frequency vs. HFO-frequency (07/24/2019 updated)
In calculating phase-amplitude coupling, a typical problem is how to determine the target frequencies in both phase and amplitude. To perform it simply, in ver.0.30 I implemented a function to generate phase-amplitude frequency-by-frequency grid plot. If you need to reduce the number of channel, do so by using EEGLAB GUI beforehand. Otherwise, this frequency scan process does not need any preprocessing by PACT, it does the job itself. One extra parameter you have to choose is highest amplitude sampling (HAS) rate, which specifies the right-tail cutoff for the amplitude distribution for each channel. Note that this is only picking up the highest amplitude after high-frequency band-pass filter, so if there is artifact with high-frequency (or broadband), HAS will pick it up. In this case, you would want to clean the data using EEGLAB function before performing this analysis.
In the example below, one can easily find that Ch21 showed the strongest PAC between 3-Hz phase and 80-Hz HFO amplitude, followed by Ch16. Ch18 also showed some PAC, but it coupled with 1.7 Hz instead of 3 Hz so this could be something different. If one chooses mean vector length to show instead of Canolty's modulation index (MI), it allows to evaluate the same measure without the effect of HFO amplitude. The calculated values are stored under EEG.pacScan.
How to obtain mean HFO gamma amplitude
- In the plot above, confirm that the peak PAC value is observed at Ch21, phase 3.2-Hz, ampltiude 80-Hz.
- Type 'EEG.pacScan' in the command line. Among the variables, find 'meanHfoAmp' This is mean HFO amplitude in microVolt. If you are not sure about dimensions, see 'dataDimensions'. We know our channel and freq-freq window of interest, which are 21, 3.2 Hz, 80 Hz, respectively. Based on these parameters of interest, we obtain indices for these parameters: 21 for the channel order, 7 for the phase freq (see 'phaseFreqEdge'--3.2Hz is between the 7th and 8th edges, so we select 7), and 1 for the HFO freq.
- We enter EEG.pacScan.meanHfoAmp(21,7,1) in the command window. It returned '35.0391' which mean the mean HFO amplitude during the selected HFO frames was 35.0391 microVolt.
Bug report, request, comment
Please post bugs and suggestions to the EEGLAB mailing list.
http://www.ncbi.nlm.nih.gov/pubmed/24110429 Makoto Miyakoshi, Arnaud Delorme, Tim Mullen, Katsuaki Kojima, Scott Makeig, Eishi Asano. Automated detection of cross-frequency coupling in the electrocorticogram for clinical inspection. Conf Proc IEEE Eng Med Biol Soc.2013.3282-3285.