significance of coherence differences

Claudia Arena c.arena at UVA.NL
Wed Sep 8 20:12:46 CEST 2010

Dear Eric Maris,

I too am confused about coherence and its statistical analysis..I am trying to 
calculate the coherence between POz and 47 other channels in a multisubject 
study (N=19) with a within-subject design to test (1) whether coherence in 
condition 'Figure' is the same as in condition 'No figure', and (2) whether 
coherence differs between 3 conditions 'Hits', 'Misses' and 'Correct rejections'. 

Either way I am not sure about a couple of things:

1) This is maybe a silly question but in your reply to Jan's post you 
state: "...You apply this test statistic to the condition-specific coherences, 
obtained by summing and normalizing the trial(taper)-specific cross-
spectra..." - You mean averaging the trial-specific cross-spectra (and trial-
specific powerspectra) right? Moreover does this mean that cfg.keeptrials can 
be set to 'no' when calculating the powerspectra and cross-spectra with 
freqanalysis(_mtmconvol)? This would be great news for me, since the 4D 
freqdata is too large to save..

2) Another related question comes from the fact that the experiment had 3 
different masking durations, so to combine the powerspectra belonging to the 
same condition (i.e. the Figs) but different mask durations we calculated 
weighted averages based on the least amount of trials in each Mask duration 
group. My question now would be whether the normalization to get the 
coherence values should be done before or after this weighing (In other words, 
should I weigh the cross-spectra or the coherence values, or does this not 

3) Now for the statistics. Again in your reply to Jan's post you say: "...For a 
single channel pair and a single frequency bin, the appropriate statistic is the 
dependent (paired) samples t-statistic or, in a nonparametric framework, the 
Wilcoxon signed rank sum test." Does this mean it is not valid to use 
freqstatistics with cfg.method = 'montecarlo' and cfg.statistic = 'depsamplesT' 
(and cfg.correctm = 'fdr' or 'cluster') if I want to test whether the coherence  
between POz (my and the 47 other channels is the same in 
different conditions, using all my frequency and time bins? Do I need to make a 

Thank you for your time.



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