PLV all in one matrix

Dear Community,

I have created a script that calculates the phase-correlation (PLV) values for every participant for every frequency.

I have added a feature so it will give me all the PLV's per participant per frequency in a matrix. Then I am copying it in excel and then will calculate the mean eventually.

Now I am doing everything manually, but i was wondering, can I make something in the script so that every frequency will be put in my matrix, and it will keep on going untill 30Hz so I can copy the whole matrix in one time?

% names of the channels you want to compute connectivity between
channel1 = 'F7';
channel2 = 'FC1';

frequencies = [9];
% frequencies = [6];
nfreq = length(frequencies);
srate = ALLEEG.srate
time  = -1:1/srate:1;     
half_wavN = (length(time)-1)/2;
all_wavelet = zeros(10, 1001); 
for idx = 1 : nfreq
    center_freq = frequencies(idx);
    wavelet   = exp(2*1i*pi*center_freq.*time) .* exp(-time.^2./(2*(4/(2*pi*center_freq))^2));
    all_wavelet(idx,:)= wavelet;
end


%%and then this is how I put it in the matrix:
filenames_TDCS_I ={'EEGLAB_Subject_102_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_104_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_110_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_112_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_116_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_118_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_120_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_122_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_124_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_128_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_132_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_138_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_140_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_148_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_150_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_152_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_154_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_156_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_158_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set','EEGLAB_Subject_164_I_REST_EC_chanrej_ep_rej_ICA pruned with ICA_ICA_clean_avref_int_int_final.set'}


phase_synchronization_all = zeros(1,length(filenames_TDCS_I)) 
for filenr=1:length(filenames_TDCS_I)
    file_name_current = char(filenames_TDCS_I(filenr))
    EEGdataset = pop_loadset('filename',file_name_current,'filepath',filepath2);    
    
    

I hope this makes sense! I(See attachments also)

Best,

Carmen

Answer 1

[Nipun]

Hi Carmen,

I understand that you want to automate the process of calculating phase-correlation (PLV) values for every participant for every frequency and store them in a matrix. Here's how you can modify your script to achieve this:

% Names of the channels you want to compute connectivity between
channel1 = 'F7';
channel2 = 'FC1';

% Frequencies to iterate over
frequencies = 1:30;
nfreq = length(frequencies);

% Preallocate phase synchronization matrix
phase_synchronization_all = zeros(nfreq, length(filenames_TDCS_I));

% Iterate over frequencies
for freq_idx = 1:nfreq
    center_freq = frequencies(freq_idx);
    
    % Generate wavelet for current frequency
    wavelet   = exp(2*1i*pi*center_freq.*time) .* exp(-time.^2./(2*(4/(2*pi*center_freq))^2));
    
    % Iterate over participants
    for filenr = 1:length(filenames_TDCS_I)
        file_name_current = char(filenames_TDCS_I(filenr));
        EEGdataset = pop_loadset('filename', file_name_current, 'filepath', filepath2);
        
        % Calculate PLV for current participant and frequency
        % (Replace the following line with your PLV calculation code)
        phase_synchronization_all(freq_idx, filenr) = calculate_PLV(EEGdataset, channel1, channel2, wavelet);
    end
end

In this modified script:

• You iterate over frequencies from 1 to 30 using frequencies = 1:30.
• For each frequency, you generate the wavelet.
• Then, you iterate over participants and calculate PLV for each frequency and each participant, storing the results in the phase_synchronization_all matrix.

Make sure to replace calculate_PLV with your actual PLV calculation code.

Let me know if you need further assistance!

Hope this helps.

Regards,

Nipun