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Hi Avi,
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<div class="">Fieldtrip uses ‘rpt’ as a generic indicator for a piece of data. Whether it is a ’trial’ in the traditional sense, i.e. related to a specific experimental event depends on the context.</div>
<div class="">If you have a long segment of data that is cut into 2-second snippets (e.g. by means of ft_redefinetrial) then FT calls the individual epochs a ’trial’.</div>
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<div class="">If you want to have an estimate of how the PLI changes during the course of the recording, you’d need to somehow use a ‘moving window’ that selects chunks of ’trials’ selectively for a per-chunk computation of the PLI. Explicitly, for instance
when you have 10 minutes of recording, chopped into 300 snippets of 2 seconds, compute the PLI in chunks of 50 trials, starting with trial 1-50, then 2-51 etc.</div>
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<div class="">If you want get an estimate for the 8-13 you can either average the PLI across frequency bins, or titrate your spectral transformation such that your estimate at ~10 captures the 7-13 frequency band. This can be achieved by appropriately specifying
the options for multitapering. For multitapering there is ample documentation on the fieldtrip website.</div>
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<div class="">Best wishes,</div>
<div class=""><br class="">
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<div class="">Jan-Mathijs<br class="">
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<blockquote type="cite" class="">
<div class="">On 4 Apr 2022, at 12:27, Avijit Chowdhury via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div class="">Dear Jan-Mathijs, </div>
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<div dir="auto" class="">Thank you for your reply.</div>
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<div dir="auto" class="">I am analysing resting state data so I don't have any "trials" as such, but that I would like to calculate PLI values for successive 2 sec segments in my data.</div>
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<div dir="auto" class="">What does cfg.keeptrials = 'yes' accomplish in this case? My idea was that since this calculates the cross-spectral density at the trial level, the subsequent PLI is also calculated at the trial level.</div>
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<div dir="auto" class="">Coming back to my initial question, how do I get the PLI across a certain frequency band (example: 8-13 hz, Alpha band) for each 2 sec segments? Currently with my script I am getting a PLI value with the dimensions : repetition * channel
* channel * frequencies (in steps of 1 hz). </div>
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<div dir="auto" class="">Best,</div>
<div dir="auto" class="">Avi<br class="">
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<div dir="ltr" class="gmail_attr">On Mon, Apr 4, 2022, 3:49 AM Schoffelen, J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space" class="">Hi Avi,
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</div>
<div class="">PLI, like any other connectivity metric needs to be computed across some unit-of-observation in order for it to make sense.</div>
<div class="">In FieldTrip, the UOs for connectivity analysis are always considered to be the trial dimension.</div>
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<div class="">In other words, no there is no way to compute a PLI for an individual trial (although you could get a ‘proxy’ for the single trial PLI by computing a so-called pseudo value, which from the top of my head (but please look this up to be sure) is
computed as: N*PLI(all) - (N-1)*PLI(loo), where PLI(avg) is the PLI computed across all repetitions, and PLI(loo) is the PLI computed using a leave-one-out strategy. You may also have a look at this paper: <a href="https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/25917516/__;!!HJOPV4FYYWzcc1jazlU!5CMvX7RGdI5GxnlGFVrRspti_kuhd2yXmnZOlooH-gvNO6VeXwkMaOK9BP0k8Nbdyns4u4Pi000NyqGfBHTEY32LGS3Sy_176Rk_RQ$" target="_blank" rel="noreferrer" class="">https://pubmed.ncbi.nlm.nih.gov/25917516/</a> or
this one: <a href="https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/17569862/__;!!HJOPV4FYYWzcc1jazlU!5CMvX7RGdI5GxnlGFVrRspti_kuhd2yXmnZOlooH-gvNO6VeXwkMaOK9BP0k8Nbdyns4u4Pi000NyqGfBHTEY32LGS3Sy_0KwV44wQ$" target="_blank" rel="noreferrer" class="">https://pubmed.ncbi.nlm.nih.gov/17569862/</a> </div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 3 Apr 2022, at 06:42, Avijit Chowdhury via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank" rel="noreferrer" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div style="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;text-decoration:none" class="">
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">Dear all,<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">I am novice to EEG analysis and I am trying to calculate Phase Lag Index for my resting state data.<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">I have redefined the data as 2 sec trials and then run ft_frequencyanalysis with “powandcsd” as cfg.output:<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg = [];<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.length = 2;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">data_trials = ft_redefinetrial(cfg, data);<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class=""><u class=""></u> <u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg = [];<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.method =<span class=""> </span><span style="color:rgb(170,4,249)" class="">'mtmfft'</span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.taper =<span class=""> </span><span style="color:rgb(170,4,249)" class="">'hanning'</span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.foilim = [8 13]; % I want to look only at alpha band<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.keeptrials =<span class=""> </span><span style="color:rgb(170,4,249)" class="">'yes'</span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.pad=<span style="color:rgb(170,4,249)" class="">'nextpow2'<span class=""> </span></span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.output=<span style="color:rgb(170,4,249)" class="">'powandcsd'</span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas;color:rgb(2,128,9)" class=""></span><span style="font-size:10pt;font-family:Consolas" class="">freq = ft_freqanalysis(cfg, data_trials);<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class=""><u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class=""> cfg = [];<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">cfg.method =<span class=""> </span><span style="color:rgb(170,4,249)" class="">'wpli'</span>;<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><span style="font-size:10pt;font-family:Consolas" class="">PLI= ft_connectivityanalysis(cfg, freq);<u class=""></u><u class=""></u></span></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">With the above script, I get an output of PLI with the dimension of trials x channel x channel x frequency.<span class=""> </span><u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">Is there a way I can get one PLI index for each trial, for each channel combination, across the frequency band I specified. Essentially, how can I get PLI values with dimensions:
trials x channel x channel<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">I am very new to this so any help is appreciated. Also, If I am trying to filter my results to only the alpha band (8-13hz), is what I am doing the correct way to achieve this?<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">Thank you,<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class="">Avi<u class=""></u><u class=""></u></div>
<div style="margin:0in;font-size:11pt;font-family:Calibri,sans-serif" class=""><u class=""></u> <u class=""></u></div>
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