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Hi Tyler,
<div class=""><br class="">
</div>
<div class="">As far as I remember the original WPLI defines the metric as an absolute quantity, which is obviously what you also requested as per the cfg that you pasted in your e-mail. Many of the classical (and also the less classical) connectivity metrics
are symmetric around the diagonal, so I don’t think that anything untowards is happening.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 13 Mar 2023, at 10:04, 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=""><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="">Dear
Jan-Mathijs,</span>
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first, I apologize if my message seemed demanding. This was not my intention as I greatly appreciate the help! Thank you very much for your answer! I implemented your suggestion and now the output is in the desired 30x30 format. </div>
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I have a follow-up question, as the values for the upper and lower triangular parts of the debiased wpli adjacency matrix (values in both directions of each channel combination) are identical. I tried numerous approaches to address this issue such as running
the same script on numerous datasets, changing the preprocessing (increase in segment length as well as less downsampling), and changing the metric to „wpli“ and „plv" but the results remain the same. Also, I checked the cfg.channelcmb, and the channels are
listed properly in both directions for each channel pair, so this also shouldn’t be the root of the issue. Lastly, as my previous dataset was preprocessed in EEGLAB, I reanalyzed the same dataset entirely using FieldTrip functions. Still, the results remain
the same. Here is the current code I use:</div>
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<blockquote type="cite" class="">
<div class="">% Load the data into FieldTrip data structure</div>
<div class="">cfg = [];</div>
<div class="">cfg.dataset = ftfile;</div>
<div class="">cfg.continuous = 'yes';</div>
<div class="">ft_data = ft_preprocessing(cfg);</div>
<div class=""><br class="">
</div>
<div class="">% Define the resampling parameters</div>
<div class="">cfg = [];</div>
<div class="">cfg.resamplefs = 250; </div>
<div class=""><br class="">
</div>
<div class="">% Resample the data</div>
<div class="">ft_data_rs = ft_resampledata(cfg, ft_data);</div>
<div class=""><br class="">
</div>
<div class="">% Cut data into multiple trials (necessary for wpli computation)</div>
<div class="">cfg = [];</div>
<div class="">cfg.length = 10; </div>
<div class="">cfg.overlap = 0;</div>
<div class="">ft_data_rs_seg = ft_redefinetrial(cfg, ft_data_rs);</div>
<div class=""><br class="">
</div>
<div class="">% Freq analysis I</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'mtmfft'; </div>
<div class="">cfg.output = 'fourier'; </div>
<div class="">cfg.taper = 'dpss'; </div>
<div class="">cfg.foi = 13:30; </div>
<div class="">cfg.keeptrials = 'yes'; </div>
<div class="">cfg.channel = 'all';</div>
<div class="">cfg.trials = 'all'; </div>
<div class="">cfg.tapsmofrq = 8; </div>
<div class="">cfg.pad = 'nextpow2'; </div>
<div class="">cfg.channelcmb = ft_channelcombination('all', ft_data_rs_seg.label, 1, 2); </div>
<div class=""><br class="">
</div>
<div class="">freq=ft_freqanalysis(cfg,ft_data_rs_seg);</div>
<div class=""><br class="">
</div>
<div class="">% Define the connectivity parameters</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'wpli_debiased'; </div>
<div class="">cfg.complex = 'abs';</div>
<div class=""><br class="">
</div>
<div class="">wpli_data = ft_connectivityanalysis(cfg, freq);</div>
</blockquote>
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Is there any mistake in the code that leads to the wpli values being identical for both directions?</div>
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All the best,</div>
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Tyler</div>
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<blockquote type="cite" class="">
<div class=""></div>
</blockquote>
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<blockquote type="cite" class="">
<div class="">
<blockquote type="cite" class="">
<div class="">Am 07.03.2023 um 16:30 schrieb Schoffelen, J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>>:</div>
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<div class="">
<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">
<div class="">Hi Tyler,</div>
<div class=""><br class="">
</div>
<div class="">Probably you should either use</div>
<div class=""><br class="">
</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>
<div class=""><br class="">
</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>
<div class=""><br class="">
</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>
<div class=""><br class="">
</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 class=""><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 class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">
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?<span class="Apple-converted-space"> </span><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 class="" style="white-space: pre;">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 class="" style="white-space: pre;">I found that this is probably due to the fact that my data is bivariate and the code states that „</span><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);"> This only
has an effect when </span></span><span class="" style="color: rgb(0, 128, 19); white-space: pre;">the input data</span></div>
<div class=""><span class="" style="color: rgb(0, 128, 19); white-space: pre;">is univariate</span><span class="" style="white-space: pre;">“.
</span></div>
<div class=""><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class=""><span class="" style="white-space: pre;">Here is the code I’ve used so far:</span></div>
<div class=""><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class="">
<div class="rtcContent">
<div class="lineNode"></div>
<blockquote type="cite" class="">
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);">% Define the resampling parameters</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg = [];</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.resamplefs = 125;
</span></div>
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);"><br class="">
</span></span></div>
<div class="lineNode"></div>
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);">% Resample the data</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">ft_data_rs = ft_resampledata(cfg, ft_data);</span></div>
<div class="lineNode"><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class="lineNode"></div>
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);">% Cut data into multiple trials</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg = [];</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.length = 1; <span class="" style="color: rgb(0, 128, 19);">
% 1 sec. segments</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.overlap = 0;</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">ft_data_rs_seg = ft_redefinetrial(cfg, ft_data_rs);</span></div>
<div class="lineNode"><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class="lineNode"></div>
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);">% Freq analysis I</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg = [];</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.method = <span class="" style="color: rgb(167, 9, 245);">
'mtmfft'</span>; <span class="" style="color: rgb(0, 128, 19);">% use multitaper frequency transformation
</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.output = <span class="" style="color: rgb(167, 9, 245);">
'powandcsd'</span>; <span class="" style="color: rgb(0, 128, 19);">% compute power spectrum and cross-spectral density</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.taper = <span class="" style="color: rgb(167, 9, 245);">
'dpss'</span>; <span class="" style="color: rgb(0, 128, 19);">% use DPSS taper window
</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.foi = 1:30; <span class="" style="color: rgb(0, 128, 19);">
% frequency range of interest</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.keeptrials = <span class="" style="color: rgb(167, 9, 245);">
'yes'</span>; <span class="" style="color: rgb(0, 128, 19);">% average over trials</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.channel = <span class="" style="color: rgb(167, 9, 245);">
'all'</span>; <span class="" style="color: rgb(0, 128, 19);">% use all channels</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.trials = <span class="" style="color: rgb(167, 9, 245);">
'all'</span>; <span class="" style="color: rgb(0, 128, 19);">% use all trials</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.tapsmofrq = 8;
<span class="" style="color: rgb(0, 128, 19);">% specify the smoothing parameter for DPSS</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.pad = <span class="" style="color: rgb(167, 9, 245);">
'nextpow2'</span>; <span class="" style="color: rgb(0, 128, 19);">% should increase computation speed
</span></span></div>
<div class="lineNode"></div>
<div class="lineNode"><span class="" style="white-space: pre;">freq=ft_freqanalysis(cfg,ft_data_rs_seg);</span></div>
<div class="lineNode"><br class="">
</div>
<div class="lineNode"></div>
<div class="lineNode"><span class="" style="white-space: pre;"><span class="" style="color: rgb(0, 128, 19);">% Define the connectivity parameters</span></span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg = [];</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.method = <span class="" style="color: rgb(167, 9, 245);">
'wpli_debiased'</span>; </span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.channelcmb = {<span class="" style="color: rgb(167, 9, 245);">'all'
</span><span class="" style="color: rgb(167, 9, 245);">'all'</span>};</span></div>
<div class="lineNode"><span class="" style="white-space: pre;">cfg.complex = <span class="" style="color: rgb(167, 9, 245);">
'abs'</span>;</span></div>
<div class="lineNode"><br class="">
</div>
<div class="lineNode"><span class="" style="white-space: pre;">wpli_data = ft_connectivityanalysis(cfg, freq);</span></div>
</blockquote>
</div>
</div>
<div class=""><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class=""><span class="" style="white-space: pre;">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 class="" style="white-space: pre;">the debiased wpli output in a 30x30 adjacency/connectivity matrix.
</span></div>
<div class=""><span class="" style="white-space: pre;"><br class="">
</span></div>
<div class=""><span class="" style="white-space: pre;">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<span class="Apple-converted-space"> </span></div>
</div>
<br class="">
</div>
</div>
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!5nYDiviMydBKAIUumUoC-7Wc0TSgaG1O1dnjKB8nSa6FSASMoLYo1RmOxS7vdHXXhw3sF9AH-4b1u-A7aVrnCIZaVO0vAZ12NGlReA$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!5nYDiviMydBKAIUumUoC-7Wc0TSgaG1O1dnjKB8nSa6FSASMoLYo1RmOxS7vdHXXhw3sF9AH-4b1u-A7aVrnCIZaVO0vAZ12NGlReA$</a><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=""></span></div>
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