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Hello,</div>
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<div style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);">
I am running into an error with the connectivity script, where the output values are NaN. See below for the code section.</div>
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%% Compute coherence
<div><br>
</div>
<div>if computecoh == 1</div>
<div> </div>
<div> if strcmp(reference,'car')</div>
<div> load([restdir 'rest_preproc_car_matched.mat'])</div>
<div> elseif strcmp(reference,'csd')</div>
<div> load([restdir 'rest_preproc_csd_matched.mat'])</div>
<div> end</div>
<div> </div>
<div> % 1. Create TFRs by condition - frequency over time</div>
<div> cfg = [];</div>
<div> cfg.channel = [lfchans rfchans lpchans rpchans];</div>
<div> cfg.output = 'fourier';</div>
<div> cfg.method = 'mtmconvol';</div>
<div> cfg.taper = 'hanning';</div>
<div> cfg.foi = 2:1:50;</div>
<div> cfg.toi = -1:0.05:3;</div>
<div> cfg.t_ftimwin = 3./cfg.foi; % [lf hf].*cfg.foi; % length of time window; number of cycles per time window</div>
<div> cfg.keeptrials = 'yes';</div>
<div> cfg.pad = 10;</div>
<div> [tfa_rest] = ft_freqanalysis(cfg,rest_preproc);</div>
<div> </div>
<div> save([conndir 'tfa_forconn_rest_' reference '.mat'],'tfa_rest');</div>
<div> </div>
<div> </div>
<div> % COMPUTE CONNECTIVITY METRICS</div>
<div> </div>
<div> % ~~ select relevant time period </div>
<div> cfg = [];</div>
<div> cfg.latency = [0.001 2];</div>
<div> [tfa_rest] = ft_selectdata(cfg, tfa_rest);</div>
<div> </div>
<div> % Coherence</div>
<div> cfg = [];</div>
<div> cfg.method = 'coh';</div>
<div> cfg.complex = 'imag'; %'abs'</div>
<div> cfg.channelcmb = ft_channelcombination('all',tfa_rest.label);</div>
<div> rest_cohconn = ft_connectivityanalysis(cfg,tfa_rest);</div>
<div> </div>
<div> save([conndir 'rest_cohconn_',reference,'.mat'],'rest_cohconn');</div>
<div> </div>
<div> clear *_coh tfa* rest_preproc</div>
<div> </div>
<div>end</div>
<div><br>
</div>
<div>% to visualize each pair's coherence values</div>
<div>% figure;imagesc(squeeze(rest_cohconn.cohspctrm(1,6,:,:))); colorbar</div>
<div><br>
</div>
<div>%% Extract coherence values</div>
<div><br>
</div>
<div>if extract == 1</div>
<div> </div>
<div> load([conndir 'rest_cohconn_',reference,'.mat']);</div>
<div> </div>
<div> % Extract channel index</div>
<div> lfchanidx=[]; rfchanidx=[]; lpchanidx=[]; rpchanidx=[];</div>
<div> for c=1:numel(lfchans)</div>
<div> lfchanidx(c) = find(strcmp(lfchans{c},rest_cohconn.label));</div>
<div> end</div>
<div> for c=1:numel(rfchans)</div>
<div> rfchanidx(c) = find(strcmp(rfchans{c},rest_cohconn.label));</div>
<div> end</div>
<div> for c=1:numel(lpchans)</div>
<div> lpchanidx(c) = find(strcmp(lpchans{c},rest_cohconn.label));</div>
<div> end</div>
<div> for c=1:numel(rpchans)</div>
<div> rpchanidx(c) = find(strcmp(rpchans{c},rest_cohconn.label));</div>
<div> end</div>
<div> </div>
<div> % identify frequency range of interest</div>
<div> lowf = find(lf == rest_cohconn.freq);</div>
<div> highf = find(hf == rest_cohconn.freq);</div>
<div> freq = [lowf:highf];</div>
<div> clear lowf highf</div>
<div> </div>
<div> % average over frequency range of interest, outputs chan x chan matrix</div>
<div> cohdata = abs(mean(mean(rest_cohconn.cohspctrm(:,:,freq,:),3),4));</div>
<div> </div>
<div> % left - frontal vs parietal</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lfchanidx)</div>
<div> for d = 1:numel(lpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),lpchanidx(d));</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> left_fvsp_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % right - frontal vs parietal</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(rfchanidx)</div>
<div> for d = 1:numel(rpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(rfchanidx(c),rpchanidx(d));</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> right_fvsp_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % frontal - right vs left</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lfchanidx)</div>
<div> for d = 1:numel(rfchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),rfchanidx(d));</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> frontal_lvsr_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % parietal - right vs left</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lpchanidx)</div>
<div> for d = 1:numel(rpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lpchanidx(c),rpchanidx(d),:);</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> parietal_lvsr_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % left frontal vs right parietal</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lfchanidx)</div>
<div> for d = 1:numel(rpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d),:);</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> lfrpcoh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % right frontal vs left parietal</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(rfchanidx)</div>
<div> for d = 1:numel(lpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(rfchanidx(c),lpchanidx(d),:);</div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> rflpcoh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> % right frontal and parietal vs left frontal and parietal</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lfchanidx)+numel(lpchanidx)</div>
<div> for d = 1:numel(rfchanidx)+numel(rpchanidx)</div>
<div> if c <= numel(lfchanidx) % left frontal</div>
<div> if d <= numel(rfchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),rfchanidx(d),:);</div>
<div> else</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d-numel(rfchanidx)),:);</div>
<div> end</div>
<div> else % left parietal</div>
<div> if d <= numel(rfchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lpchanidx(c-numel(lfchanidx)),rfchanidx(d),:);</div>
<div> else</div>
<div> cohtmp(cnt,1) = cohdata(lpchanidx(c-numel(lfchanidx)),rpchanidx(d-numel(rfchanidx)),:);</div>
<div> end</div>
<div> end</div>
<div> </div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> leftvsright_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div> </div>
<div> % frontal vs parietal (left and right)</div>
<div> cnt = 1;</div>
<div> for c = 1:numel(lfchanidx)+numel(rfchanidx)</div>
<div> for d = 1:numel(lpchanidx)+numel(rpchanidx)</div>
<div> if c <= numel(lfchanidx) % left</div>
<div> if d <= numel(lpchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),lpchanidx(d),:);</div>
<div> else</div>
<div> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d-numel(lpchanidx)),:);</div>
<div> end</div>
<div> else % right</div>
<div> if d <= numel(rfchanidx)</div>
<div> cohtmp(cnt,1) = cohdata(rfchanidx(c-numel(lfchanidx)),lpchanidx(d),:);</div>
<div> else</div>
<div> cohtmp(cnt,1) = cohdata(rfchanidx(c-numel(lfchanidx)),rpchanidx(d-numel(lpchanidx)),:);</div>
<div> end</div>
<div> end</div>
<div> </div>
<div> cnt = cnt + 1;</div>
<div> end</div>
<div> end</div>
<div> % ~ average across electrode pairs</div>
<div> frontalvsparietal_coh = mean(cohtmp); clear cohtmp</div>
<div> </div>
<div>end</div>
<div><br>
</div>
<div>% Save File</div>
<div>filename = strcat('rest_cohconn_roi_',num2str(lf),'_',num2str(hf),'_',reference,'.mat');</div>
<div>save([conndir filename], '*_coh','*chans');</div>
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</div>
Thank you for your time and help.</div>
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Sincerely,</div>
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