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<div class="">Hi Tyler,</div>
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<div class="">Probably you should either use</div>
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</div>
cfg.output = ‘fourier’ in the call to ft_freqanalysis, or
<div class=""><br class="">
</div>
<div class="">specify cfg.channelcmb in your call to ft_freqanalysis should do it. </div>
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</div>
<div class="">(actually, the quote from the help docstring of (what I asume to be) ft_connectivityanalysis - which you pasted into your e-mail, sums up the above: cfg.channelcmb in ft_connectivityanalysis does not have a functional effect, because the input
data was NOT univariate (no ‘fourier’ in output), but the recipe for ft_freqanalysis did not specify the channelcmb, so the data were detected to be bivariate (‘powandcsd’), but only with bivariate auto-pairs)</div>
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</div>
<div class="">Please note, that questions asked on this discussion list are only answered by people on a voluntary basis. Nobody has it as their job to answer to this list, so you shouldn’t expect people to answer, and certainly not within a particular time
frame. Also, the quality of the question matters, and to be honest the original question had some room for improvement.</div>
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</div>
<div class="">Best wishes and good luck with your analysis,</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 7 Mar 2023, at 15:25, Tyler Durdern via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Dear all,
<div class=""><br class="">
</div>
<div class="">I asked this question but I did not receive a response yet:</div>
<div class=""><br class="">
<div class="">
<div class="">
<blockquote type="cite" class="">I computed the debiased weighted phase lag index for all channel combinations of a 30-channel EEG resting state recording. The output file (wpli_debiasedspctrm) has the following dimensions (435x30). I subsequently averaged
the file across the second dimension to get an average debiased wpli estimate across the frequency band of interest. Now, I want to put this estimate into an adjacency matrix format (30x30) so I can illustrate the connectivity matrix using e.g. imagesc in
Matlab. Is there a way I can achieve this in fieldtrip? <br class="">
</blockquote>
<div class=""><br class="">
</div>
I tried a few approaches in the mean time but I cannot seem to get the results I want. Using a 30-channel EEG recording, I expect a 900x30 output variable corresponding to wpli values for all possible channel combinations (even identical ones) per frequency
in both directions (e.g. Cz-Fz and Fz-Cz). I tried to achieve this using f<span style="white-space: pre;" class="">t_channelcombination and although this yields the correct channel combinations, it doesn’t change the wpli output. Looking into the code</span></div>
<div class=""><span style="white-space: pre;" class="">I found that this is probably due to the fact that my data is bivariate and the code states that „</span><span style="white-space: pre;" class=""><span style="color: rgb(0, 128, 19);" class=""> This only
has an effect when </span></span><span style="color: rgb(0, 128, 19); white-space: pre;" class="">the input data</span></div>
<div class=""><span style="color: rgb(0, 128, 19); white-space: pre;" class="">is univariate</span><span style="white-space: pre;" class="">“.
</span></div>
<div class=""><span style="white-space: pre;" class=""><br class="">
</span></div>
<div class=""><span style="white-space: pre;" class="">Here is the code I’ve used so far:</span></div>
<div class=""><span style="white-space: pre;" class=""><br class="">
</span></div>
<div class="">
<div class="rtcContent">
<div class="lineNode"></div>
<blockquote type="cite" class="">
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class="">% Define the resampling parameters</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg = [];</span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.resamplefs = 125;
</span></div>
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class=""><br class="">
</span></span></div>
<div class="lineNode"><!--[if mso]><br><![endif]--></div>
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class="">% Resample the data</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">ft_data_rs = ft_resampledata(cfg, ft_data);</span></div>
<div class="lineNode"><span style="white-space: pre" class=""><br class="">
</span></div>
<div class="lineNode"><!--[if mso]><br><![endif]--></div>
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class="">% Cut data into multiple trials</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg = [];</span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.length = 1; <span style="color: rgb(0, 128, 19);" class="">
% 1 sec. segments</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.overlap = 0;</span></div>
<div class="lineNode"><span style="white-space: pre" class="">ft_data_rs_seg = ft_redefinetrial(cfg, ft_data_rs);</span></div>
<div class="lineNode"><span style="white-space: pre" class=""><br class="">
</span></div>
<div class="lineNode"><!--[if mso]><br><![endif]--></div>
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class="">% Freq analysis I</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg = [];</span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.method = <span style="color: rgb(167, 9, 245);" class="">
'mtmfft'</span>; <span style="color: rgb(0, 128, 19);" class="">% use multitaper frequency transformation
</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.output = <span style="color: rgb(167, 9, 245);" class="">
'powandcsd'</span>; <span style="color: rgb(0, 128, 19);" class="">% compute power spectrum and cross-spectral density</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.taper = <span style="color: rgb(167, 9, 245);" class="">
'dpss'</span>; <span style="color: rgb(0, 128, 19);" class="">% use DPSS taper window
</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.foi = 1:30; <span style="color: rgb(0, 128, 19);" class="">
% frequency range of interest</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.keeptrials = <span style="color: rgb(167, 9, 245);" class="">
'yes'</span>; <span style="color: rgb(0, 128, 19);" class="">% average over trials</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.channel = <span style="color: rgb(167, 9, 245);" class="">
'all'</span>; <span style="color: rgb(0, 128, 19);" class="">% use all channels</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.trials = <span style="color: rgb(167, 9, 245);" class="">
'all'</span>; <span style="color: rgb(0, 128, 19);" class="">% use all trials</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.tapsmofrq = 8; <span style="color: rgb(0, 128, 19);" class="">
% specify the smoothing parameter for DPSS</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.pad = <span style="color: rgb(167, 9, 245);" class="">
'nextpow2'</span>; <span style="color: rgb(0, 128, 19);" class="">% should increase computation speed
</span></span></div>
<div class="lineNode"><!--[if mso]><br><![endif]--></div>
<div class="lineNode"><span style="white-space: pre" class="">freq=ft_freqanalysis(cfg,ft_data_rs_seg);</span></div>
<div class="lineNode"><br class="">
</div>
<div class="lineNode"><!--[if mso]><br><![endif]--></div>
<div class="lineNode"><span style="white-space: pre" class=""><span style="color: rgb(0, 128, 19);" class="">% Define the connectivity parameters</span></span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg = [];</span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.method = <span style="color: rgb(167, 9, 245);" class="">
'wpli_debiased'</span>; </span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.channelcmb = {<span style="color: rgb(167, 9, 245);" class="">'all'
</span><span style="color: rgb(167, 9, 245);" class="">'all'</span>};</span></div>
<div class="lineNode"><span style="white-space: pre" class="">cfg.complex = <span style="color: rgb(167, 9, 245);" class="">
'abs'</span>;</span></div>
<div class="lineNode"><br class="">
</div>
<div class="lineNode"><span style="white-space: pre" class="">wpli_data = ft_connectivityanalysis(cfg, freq);</span></div>
</blockquote>
</div>
</div>
<div class=""><span style="white-space: pre;" class=""><br class="">
</span></div>
<div class=""><span style="white-space: pre;" class="">To summarize: I would like to compute debiased wpli for all channels (even identical ones) in both directions. Further, I would like to store
</span></div>
<div class=""><span style="white-space: pre;" class="">the debiased wpli output in a 30x30 adjacency/connectivity matrix.
</span></div>
<div class=""><span style="white-space: pre;" class=""><br class="">
</span></div>
<div class=""><span style="white-space: pre;" class="">As I am still quite new to FieldTrip I am stuck here and I would really appreciate your help on this issue.</span></div>
<div class=""><br class="">
Thanks in advance and all the best,<br class="">
<br class="">
Tyler </div>
</div>
<br class="">
</div>
</div>
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</blockquote>
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