Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Mon Oct 2 21:03:53 CEST 2006

Hi Peter

> I’m trying to do clusterrandanalysis on TFR data with the cfg.  
> statistic=’actvsblT’ option. The tutorial ‘Cluster-level  
> randomization tests’ gives an example in which separate TFRs are  
> calculated for activation and baseline data. The  
> clusterrandanalysis.m documentation also states that two datasets  
> must be passed.

I am not that familiar with comparing activation versus baseline  
using the actvsblT statistic (it was implemented by Eric) but as I  
understand it, the rationale behind it is that all timepoints in the  
baseline are equivalent to all timepoints in the activation period.  
I.e. there is no intrinsic reason to compare one specific baseline  
timepoint with one specific timepoint in the active period, hence it  
implements a comparison in which all timepoints in the baseline are  
collapsed/averaged, and the active period is compared to this average.

 From the FT homepage documentation ( 

>> With cfg.statistic=’actvsblT’, we choose the so-called activation- 
>> versus-baseline T-statistic. By means of this statistic, we  
>> compare the power in every (channel, frequency, time)-element in  
>> the activation period with the corresponding average power  
>> (average over time) in the baseline period. The comparison of the  
>> activation and the average baseline power is performed by means of  
>> a pairwise T-statistic, with the pairs corresponding to the trials.

However, the approach that I usually take (and also explain to other  
people here) for comparing two time windows in the same dataset is to  
copy the dataset into a dummy dataset and shift the timeaxis of the  
dummy dataset. E.g.

dat = preprocessing(..)
avg = timelockanalysis(..) % with keeptrials
act = avg;
bas = avg;
bas.time = bas.time + 0.500;   % shift the time axis, here the sample  
corresponding with -500ms is shifted to 0ms
stat = clusterrandanalysis(cfg, bas, act)

The statistisc then becomes a regular depsamplesT (i.e. paired data  
in the baseline and activation window). E.g. in the above example you  
could do

plot(act.time, act.avg, 'r'); % in red
hold on
plot(act.time, act.avg, 'b'); % in blue

and you would see the two ERPs shifted in time. This plot also makes  
it easy to identify the timewindow in which to do the statistical  
test (default is to take all overlapping time that is present in the  
input data).

> However, I’d like to make the activation vs baseline comparison  
> work for baseline and activation TF windows identified in single  
> TFRs that include a prestimulus and a poststimulus period. To do  
> so, I used cfg. latency, cfg. frequency and cfg. keepindividual  
> with freqgrandaverage to create separate datastructures for the  
> baseline and activation timefrequency windows of interest.

Here I cannot follow you. You have two conditions, each with a  
baseline and an active period. What is the comparison taht you want  
to make? I would presume that you do not expect differences in the  
baseline. If there were an a priori difference in the baseline, then  
a difference in the active period would seem trivial to me. So to me  
teh logical assumption would be that the baselines are the same and  
that you want to compare either the whole time interval or (equally  
valid) only the active period.

I can also imagine that you want to compare the TFR data in the  
active window after correcting for eventual differences in the  
baseline. This would involve first doing a (single trial) baseline  
correction (expressing the power in each trial as relative number  
compared to the average in the baseline). In FT we have the  
freqbaseline function, however, that function sofar did not support  
single-trial baseline coprrections (only averaged powspctrm would be  
corrected). Please find attached a freqbaseline that will also do it  
on single trial powspectra.

hope this helps,

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