freqbaseline & zscore

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Mon Dec 4 10:55:42 CET 2006

On 30 Nov 2006, at 17:42, Thomas Thesen wrote:
> In version 20060605 of FT, there is an option for cf.baselinetype =
> zscore; but it is commented out in freqbaseline.m. Is there a
> specific reason for it, i.e. is the code for computing a zscore for
> baseline vs active not correct?
The code itself is correct, but I suspect the reason for it being
commented out (and not being documented) is that the behaviour of the
z-values thus computed are not exactly what you expect from a
standard normal distribution. The estimated power values in the
baseline are not independent (since in general overlapping time-
windows), resulting in an underestimated variance estimate.

A more appropriate estimate for the variance in the power would be
obtained from the baseline value over trials: e.g. something like this
  for each trial, compute avg power within baseline
  over all trials, compute mean power (1)
  over all trials, compute variance/stdev in power (2)
  for the average over all trials, for each timepoint subtract mean
of baseline (1) and divide by stdev (2)

That requires single trial power as input and average power as
output, which does not fit very well in the freqbaseline function.
> s there an inbuilt option to plot the spectrograms with
> multiplotTFR funcions 'as they are', i.e. without any baseline
> operations, just the raw values. So far I've been using imagesc on
> the data matrix, but would like to plot them in an arrangement
> specified by the .lay file.
multiplotTFR has the option cfg.baseline, which by default is 'no'.
So that should give you the desired behaviour.

> nd is there a way to compute a 2D representation of the frequency
> spectrum of a particular channel? Like a typical FFT plot with
> frequency on the x axis and power on the y axis?

That is done using multiplotER. The xxER functions (also topoplot)
work both on ERP and on frequency spectra (with no time).

best regards,

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