[Eeglablist] newtimef settings and output

[Jeff Johnson]

Greetings-

I am using newtimef to calculate the ersp for a set of data where the
baseline will be taken from a temporally non-adjacent time window, and I had
a couple of questions about the appropriate settings to use, and about the
outputs of newtimef using different settings. Our experiment involves the
sequential presentation of 4 to-be-remembered objects, followed by a 3-sec
memory delay, the appearance of a probe object, and a short (1 sec) ITI. We
are interested in exploring sustained neural oscillations during the delay
interval, and are using a portion of the ITI as our baseline. Because the
ITI begins ~4200 ms before the delay period starts, we are calculating the
ersp for the delay period (+-500 ms) and the ITI separately, and doing the
baseline subtraction as a separate step, following the ersp calculation.
This raises a few questions:

First, a clarification question: If I leave 'baseline' unspecified, does
newtimef use the mean across the entire time window for each frequency as
the baseline? If this is correct, it seems like this method of baseline
correction would tend to mask the presence of sustained power increases that
may be present throughout the interval in question. For instance, if I have
a steady elevation in power of 12 mV^2/Hz throughout the delay in some
frequency band, the mean across the time window will be ~12 as well, and
when I do the subtraction, the resulting value will be ~0.

If I have this right, it seems like the appropriate thing to do would be to
set 'baseline' to 'NaN' for both the delay and the ITI, and then do the
subtraction using these "raw" power values. However, when I do this, I
notice that all the power values (the values in 'ersp') I get for either the
delay period or ITI (before doing the baseline subtraction) are negative,
although the overall pattern looks very similar to what I get when I use
comparable settings using the ft_freqanalysis routines in fieldtrip, just
shifted down by some amount. Is it normal for the output to be negative, or
is this just something weird happening with my data or analysis pipeline?

In case it's relevant, here are samples of the code I'm using to do the
time-frequency analysis in EEGLab:

%%

[ersp,itc,powbase,times,freqs,
tfdata] = pop_newtimef(EEG, 1, chan, [-500 3500], 0, ...
            'type','phasecoher','padratio',4,
'timesout',100,'plotphase','off','plotersp','off','plotitc','off','freqs',[5
30],'baseline',NaN);

%%

And what I think is the approximately equivalent procedure in Fieldtrip
(some specifics are likely different, such as the number of cycles used to
estimate power for each frequency--I'm not sure exactly how to specify this
when using Hanning windows in eeglab--and the time steps):

%%
        cfg                  = [];
        cfg.output       = 'pow';
        cfg.channel      = 'all';
        cfg.method       = 'mtmconvol';
        cfg.taper           = 'hanning';
        cfg.foi               = 5:30;
        cfg.t_ftimwin     = 3./cfg.foi;  %3 cycles per freq
        cfg.toi                = -.5:0.05:3.5; % 50 ms window
        cfg.keeptrials    = 'no';

       TFRHann = ft_freqanalysis(cfg,data);

%%

I think this about covers it. Any help would be greatly appreciated.

Thanks,
Jeff


-- 

Jeffrey S. Johnson, Ph.D.
Postdoctoral Fellow
Department of Psychiatry
University of Wisconsin-Madison
6001 Research Park Blvd.
Madison, WI 53719

Email: jsjohnson3 at wisc.edu
Office phone: 608-265-8961
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