[Eeglablist] newtimef settings and output

[Arnaud Delorme]

Dear Jeff,

> 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?

No, newtimef uses by default the pre-stimulus period.

> 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?

No, the output should not be negative. The difference with Fieldtrip might be the scaling. When using a baseline, the default scaling in EEGLAB is dB although you can also use percentage of baseline or z-score.

Your Fieldtrip code uses multitaper it seems which is another difference (it is FFT in your newtimef call below). You may use multitaper in EEGLAB using the old timef function.

Best regards,

A. Delorme

> [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
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