# Output of mscohere function

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Satya Gopal on 12 Nov 2019
Commented: Satya Gopal on 13 Nov 2019
Hi all,
I have a doubt with regards to mscohere function output in matlab. I have 64 channel EEG data to extract coherence data for. Which means I would need a 64x64 matrix output for a particular frequency band say 8 to 13 Hz. I went through the documentation of mscohere function sveral times. One thing that I saw was that mscohere Cxy part can either be a vector, matrix or 3-D array. When I use the following code to calculate coherence between just two channels, channel 20 and channel 50, I get a 501×1 single column vector:
ch1 = 20;
ch2 = 50;
window = 2*EEG.srate; % create 2 sec epochs
noverlap = 0; % overlap
nfft = window*2; % zero-padding factor 2 for smoothing
fs = EEG.srate;
[Cxy,F] = mscohere(EEG.data(ch1,:),EEG.data(ch2,:),window,noverlap,nfft,fs);
Cxy
Cxy =
501×1 single column vector
0.0003
0.0060
0.0042
0.0003
0.0047 % I copied the first few values only to show the output I am getting
Can someone explain this output to me? Are these coherence values between two channels at 501 different frequency points (I'm just guessing. Not sure!)? Also, how do I input the frequency band of my interest like 8-13 Hz and calculate coherence just for that? Are there more steps in calculating coherence in matlab? How do I get a single value (between 0 to 1) for channel 20 x channel 50 coherence for 8-13 Hz frequency band?
I hope my question makes sense. Please let me know if I need to explain anything further.
Thanks!
Satya

Daniel M on 12 Nov 2019
Yes, these are the coherence values between the two channels at the frequencies returned in F. You can manually set the frequencies that you wish, for example F = [8:0.5:13]. The help section indicates this.
% [Cxy,F] = MSCOHERE(X,Y,WINDOW,NOVERLAP,F,Fs) computes the coherence
% estimate at the physical frequencies contained in the vector F. F must
% be expressed in hertz and have at least two elements.
Then you can average the output to get the total coherence over that band.

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Satya Gopal on 13 Nov 2019
Thank you for your answer, Daniel! I tried setting the frequencies manually with F and I am getting fewer values. I just have a small doubt. Why don't we use F=[8:13] but put F=[8:0.5:13]? Is it because we get a better frequency resolution or smoothening?
Yes, I will check the Fieldtrip option as well!
Daniel M on 13 Nov 2019
Because interesting things in EEG don't happen at the just the discrete frequencies, e.g. 8:13. They happen at any frequency. That's why we sample with a smaller step. You can choose a step size that works for you.
Satya Gopal on 13 Nov 2019
Thanks again, Daniel! That makes sense! I really appreciate your effort in explaining things.