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Hi Michelle,
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<div class="">In order to be able to think along, you’d need to pinpoint us to where the problem occurs. The pasted script is simply too long.</div>
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<div class="">E.g: What’s the nature of the data? i.e. how many trials etc. -> if there’s only a single trial, Fieldtrip will probably return a coherence that is 1 (or perhaps NaN). The reason for this is that coherence is to be computed across observations,
and FieldTrip uses only the ’trial’ as observation dimension, not time.</div>
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<div class="">Also, as you may have seen in the documentation about time-frequency decomposition: TFRs will contain NaNs for those time-frequency points at which the specified time-window is not completely filled with data. However, I don’t know whether localized
NaNs in the data will spread to other time-frequency points as well during the coherence computation.</div>
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<div class="">Good luck,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 26 Mar 2021, at 21:01, Yee Wong <<a href="mailto:ywong252@uwo.ca" class="">ywong252@uwo.ca</a>> wrote:</div>
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Hello,</div>
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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
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<div class="">if computecoh == 1</div>
<div class=""> </div>
<div class=""> if strcmp(reference,'car')</div>
<div class=""> load([restdir 'rest_preproc_car_matched.mat'])</div>
<div class=""> elseif strcmp(reference,'csd')</div>
<div class=""> load([restdir 'rest_preproc_csd_matched.mat'])</div>
<div class=""> end</div>
<div class=""> </div>
<div class=""> % 1. Create TFRs by condition - frequency over time</div>
<div class=""> cfg = [];</div>
<div class=""> cfg.channel = [lfchans rfchans lpchans rpchans];</div>
<div class=""> cfg.output = 'fourier';</div>
<div class=""> cfg.method = 'mtmconvol';</div>
<div class=""> cfg.taper = 'hanning';</div>
<div class=""> cfg.foi = 2:1:50;</div>
<div class=""> cfg.toi = -1:0.05:3;</div>
<div class=""> cfg.t_ftimwin = 3./cfg.foi; % [lf hf].*cfg.foi; % length of time window; number of cycles per time window</div>
<div class=""> cfg.keeptrials = 'yes';</div>
<div class=""> cfg.pad = 10;</div>
<div class=""> [tfa_rest] = ft_freqanalysis(cfg,rest_preproc);</div>
<div class=""> </div>
<div class=""> save([conndir 'tfa_forconn_rest_' reference '.mat'],'tfa_rest');</div>
<div class=""> </div>
<div class=""> </div>
<div class=""> % COMPUTE CONNECTIVITY METRICS</div>
<div class=""> </div>
<div class=""> % ~~ select relevant time period</div>
<div class=""> cfg = [];</div>
<div class=""> cfg.latency = [0.001 2];</div>
<div class=""> [tfa_rest] = ft_selectdata(cfg, tfa_rest);</div>
<div class=""> </div>
<div class=""> % Coherence</div>
<div class=""> cfg = [];</div>
<div class=""> cfg.method = 'coh';</div>
<div class=""> cfg.complex = 'imag'; %'abs'</div>
<div class=""> cfg.channelcmb = ft_channelcombination('all',tfa_rest.label);</div>
<div class=""> rest_cohconn = ft_connectivityanalysis(cfg,tfa_rest);</div>
<div class=""> </div>
<div class=""> save([conndir 'rest_cohconn_',reference,'.mat'],'rest_cohconn');</div>
<div class=""> </div>
<div class=""> clear *_coh tfa* rest_preproc</div>
<div class=""> </div>
<div class="">end</div>
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<div class="">% to visualize each pair's coherence values</div>
<div class="">% figure;imagesc(squeeze(rest_cohconn.cohspctrm(1,6,:,:))); colorbar</div>
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<div class="">%% Extract coherence values</div>
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<div class="">if extract == 1</div>
<div class=""> </div>
<div class=""> load([conndir 'rest_cohconn_',reference,'.mat']);</div>
<div class=""> </div>
<div class=""> % Extract channel index</div>
<div class=""> lfchanidx=[]; rfchanidx=[]; lpchanidx=[]; rpchanidx=[];</div>
<div class=""> for c=1:numel(lfchans)</div>
<div class=""> lfchanidx(c) = find(strcmp(lfchans{c},rest_cohconn.label));</div>
<div class=""> end</div>
<div class=""> for c=1:numel(rfchans)</div>
<div class=""> rfchanidx(c) = find(strcmp(rfchans{c},rest_cohconn.label));</div>
<div class=""> end</div>
<div class=""> for c=1:numel(lpchans)</div>
<div class=""> lpchanidx(c) = find(strcmp(lpchans{c},rest_cohconn.label));</div>
<div class=""> end</div>
<div class=""> for c=1:numel(rpchans)</div>
<div class=""> rpchanidx(c) = find(strcmp(rpchans{c},rest_cohconn.label));</div>
<div class=""> end</div>
<div class=""> </div>
<div class=""> % identify frequency range of interest</div>
<div class=""> lowf = find(lf == rest_cohconn.freq);</div>
<div class=""> highf = find(hf == rest_cohconn.freq);</div>
<div class=""> freq = [lowf:highf];</div>
<div class=""> clear lowf highf</div>
<div class=""> </div>
<div class=""> % average over frequency range of interest, outputs chan x chan matrix</div>
<div class=""> cohdata = abs(mean(mean(rest_cohconn.cohspctrm(:,:,freq,:),3),4));</div>
<div class=""> </div>
<div class=""> % left - frontal vs parietal</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lfchanidx)</div>
<div class=""> for d = 1:numel(lpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),lpchanidx(d));</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> left_fvsp_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % right - frontal vs parietal</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(rfchanidx)</div>
<div class=""> for d = 1:numel(rpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(rfchanidx(c),rpchanidx(d));</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> right_fvsp_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % frontal - right vs left</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lfchanidx)</div>
<div class=""> for d = 1:numel(rfchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),rfchanidx(d));</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> frontal_lvsr_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % parietal - right vs left</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lpchanidx)</div>
<div class=""> for d = 1:numel(rpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lpchanidx(c),rpchanidx(d),:);</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> parietal_lvsr_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % left frontal vs right parietal</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lfchanidx)</div>
<div class=""> for d = 1:numel(rpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d),:);</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> lfrpcoh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % right frontal vs left parietal</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(rfchanidx)</div>
<div class=""> for d = 1:numel(lpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(rfchanidx(c),lpchanidx(d),:);</div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> rflpcoh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> % right frontal and parietal vs left frontal and parietal</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lfchanidx)+numel(lpchanidx)</div>
<div class=""> for d = 1:numel(rfchanidx)+numel(rpchanidx)</div>
<div class=""> if c <= numel(lfchanidx) % left frontal</div>
<div class=""> if d <= numel(rfchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),rfchanidx(d),:);</div>
<div class=""> else</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d-numel(rfchanidx)),:);</div>
<div class=""> end</div>
<div class=""> else % left parietal</div>
<div class=""> if d <= numel(rfchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lpchanidx(c-numel(lfchanidx)),rfchanidx(d),:);</div>
<div class=""> else</div>
<div class=""> cohtmp(cnt,1) = cohdata(lpchanidx(c-numel(lfchanidx)),rpchanidx(d-numel(rfchanidx)),:);</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> </div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> leftvsright_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class=""> </div>
<div class=""> % frontal vs parietal (left and right)</div>
<div class=""> cnt = 1;</div>
<div class=""> for c = 1:numel(lfchanidx)+numel(rfchanidx)</div>
<div class=""> for d = 1:numel(lpchanidx)+numel(rpchanidx)</div>
<div class=""> if c <= numel(lfchanidx) % left</div>
<div class=""> if d <= numel(lpchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),lpchanidx(d),:);</div>
<div class=""> else</div>
<div class=""> cohtmp(cnt,1) = cohdata(lfchanidx(c),rpchanidx(d-numel(lpchanidx)),:);</div>
<div class=""> end</div>
<div class=""> else % right</div>
<div class=""> if d <= numel(rfchanidx)</div>
<div class=""> cohtmp(cnt,1) = cohdata(rfchanidx(c-numel(lfchanidx)),lpchanidx(d),:);</div>
<div class=""> else</div>
<div class=""> cohtmp(cnt,1) = cohdata(rfchanidx(c-numel(lfchanidx)),rpchanidx(d-numel(lpchanidx)),:);</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> </div>
<div class=""> cnt = cnt + 1;</div>
<div class=""> end</div>
<div class=""> end</div>
<div class=""> % ~ average across electrode pairs</div>
<div class=""> frontalvsparietal_coh = mean(cohtmp); clear cohtmp</div>
<div class=""> </div>
<div class="">end</div>
<div class=""><br class="">
</div>
<div class="">% Save File</div>
<div class="">filename = strcat('rest_cohconn_roi_',num2str(lf),'_',num2str(hf),'_',reference,'.mat');</div>
<div class="">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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<span style="font-size: 12pt; font-family: "Times New Roman", Times, serif;" class="">Michelle (Yee Suet) Wong</span></div>
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<span style="font-family: "Times New Roman", Times, serif;" class=""></span><span style="font-size: 12pt; font-family: "Times New Roman", Times, serif;" class="">BHK, MSc, PhD Candidate</span></div>
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<span style="font-family: "Times New Roman", Times, serif;" class=""></span><span style="font-size: 12pt; font-family: "Times New Roman", Times, serif;" class="">School of </span><font color="#212121" face="Courier New, monospace" class=""><span style="font-family: "Times New Roman", Times, serif;" class="">Kinesiology </span></font></div>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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