[FieldTrip] Connectitivy Analysis - partial directed coherence

[Barbara Schorr]

Dear Fieldtrippers



Here the introduction to my problem (I hope I can make myself clear):

I am doing a connectivity analysis (partial directed coherence) and obtain as a result following array:



connectivity = 

label:{51x1}
dimord: 'chan_chan_freq'
pdcspctrm: [51x51x101]
freq: [1x101 double]
cfg: [1x1 struct]




I have 51 channels in my analysis. I want to find out the outflow from frontal to parietal regions.
So what I did next was defining which channels belong to frontal and which to parietal regions (note: the sensor layout of the sensor net is really random), e.g.:



Frontal = { 'E5' 'E6' 'E197' 'E198'}
Parietal = { 'E77' 'E78' 'E89' 'E163'}




Next step: find outflow from each Frontal to each Parietal channels


In order to do this I need to look in "connectivity.pdspctrm" for the pdc value: 

find all the channels in "Frontal" and "Parietal" in the original "connectivity" in order to find there the corresponding pdc values:


"frontal" is a vector with indices of the channels in the connectivity.label channel list (same with "parietal")

frontal = zeros(4,1)

for l=1:4
    channelposition = find(ismember(connectivity.label, Frontal{l}) == 1);
    if isfinite(channelposition);

        if isfinite (ismember(connectivity.label, Frontal{l}) == 1, frontal (l,1) = find(ismember(connectivity.label, Frontal{l}) ==1); else frontal(l,1) = NaN; end

    else
    end
end



I get: frontal = 

1
2
10
11

parietal = zeros(4,1)

for l=1:4
    channelposition = find(ismember(connectivity.label, Parietal {l}) == 1);
    if isfinite(channelposition);

        if isfinite (ismember(connectivity.label, Parietal{l}) == 1, parietal  (l,1) = find(ismember(connectivity.label, Parietal{l}) ==1); else parietal(l,1) = NaN; end

    else
    end
end



I get: parietal = 

9
14
20
31


If I want to know now the outflow from E5 to E77 i would have to enter this as follows:

Outflow = connectivity.pdcsptrm(1,9,5)  %5 is here just an example for the frequency of interest

and I would get a value, e.g. 

ans = 0.567

(This worked totally fine!)




 >>>>>>>>>>>>>Now my Problem: <<<<<<<<<<<<<<

I don't want to know the outflow from a single electrode to another, but the average outflow from frontal to parietal for the whole Alpha  frequencyband:

So my line of code would look like this:


Outflow = connectivity.pdcspctrm(frontal',parietal',5:16)



I tried eval (eventhough it is not elegant, but it's the only thing I could think about that might work):



Outflow = eval ([ 'mean(mean(mean(connectivity.pdcspctrm(' num2str(frontal') ',' num2str(parietal'), 5:16))))' ])


When I enter it as follows:

Outflow = mean(mean(mean(connectivity.pdcspctrm([1 2 10 11], [9 14 20 31], 5:16))))

it works fine.



But the vectors frontal and parietal will contain upt to 30 indices each, so typing them is not an option.

I tried everything else I could think of (different parethesis etc.).

Maybe someone can help me out here??

Thanks a lot!!