<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Hweeling,<div><br></div><div>sorry to have been so unclear.</div><div>Unfortunately, you'll have to leave the prepared field trip code a bit to compute the phase deviance.</div><div>What you'll want to do is:</div><div><br></div><div><div>1. Compute the Phase for all channels and trials: </div><div><span class="Apple-tab-span" style="white-space:pre">       </span>Do a mtmfft with ft_freqanalysis and take the angle</div><div>2. For each trial, compute the phase difference between all channels:</div><div><span class="Apple-tab-span" style="white-space:pre">      </span>Use the circa_dist-function from the CircStat-Toolbox (Ask Google for the link)</div><div>3. For each combination, compute the mean over trials:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Use the circa_mean function from the above mentioned toolbox</div><div>4. For each combination, compute the deviance from the mean</div><div><span class="Apple-tab-span" style="white-space:pre">       </span>Again, circa_dist is your friend here.</div><div><br></div><div>Again, PLV or Coherence don't work on the single trial level, thus ft_connectivityanalysis will not work for you.</div><div><br></div><div>Good Luck,</div><div><br></div><div>Julian</div><div><br></div><div><div>Am 22.09.2014 um 10:32 schrieb Hwee Ling Lee:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear Roey, Julian and Tobias,<div><br></div><div>Thanks for the feedback.</div><div><br></div><div>Given your suggestions, I now intend to try to calculate the deviation of single trials from the mean phase difference (PLV). Pardon my ignorance, however, I still experience some problems with calculating plv for single trials.</div><div><br></div><div>Using this code to extract PLV:</div><div><br></div><div><div>    cfg                 = [];</div><div>    cfg.trials          = 'all';</div><div>    cfg.keeptrials      = 'yes';</div><div>    cfg.channel         = {'all'};</div><div>    cfg.removemean      = 'yes';   </div><div>    cfg.method           = 'plv';</div><div>    cfg.channelcmb       = {cfg.channel, cfg.channel};   </div><div>    HLF_pre_c200plv      = ft_connectivityanalysis(cfg, HLF_pre_c200);</div></div><div><br></div><div>Although I've specified to keep individual trials, ft_connectivityanalysis still show averaged PLV across trials for the output. Could anyone of you, or someone else, kindly highlight my mistake in my calculation?</div><div><br></div><div>Thank you very much!</div><div><br></div><div>Best wishes,</div><div>Hweeling</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 18 September 2014 16:39, Tobias Staudigl <span dir="ltr"><<a href="mailto:tobias.staudigl@uni-konstanz.de" target="_blank">tobias.staudigl@uni-konstanz.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <div>Dear Hweeling, <br>
      <br>
      I agree with Roey that coherence/PLV cannot be calculated for
      individual trials. <br>
      However, you could try to use the deviation (in each single trial)
      from the mean phase as an approximation.<br>
      <br>
      Good luck!<br>
      Tobias<br>
      <br>
      <br>
      <br>
      Am 18.09.2014 15:32, schrieb Roey Schurr:<br>
    </div><div><div class="h5">
    <blockquote type="cite">
      <div dir="ltr">Dear Hweeling,
        <div><br>
        </div>
        <div>Unfortunately I am not yet familiar with the PPC measure,
          but I guess that being a pairwise phase <b>consistancy</b> measure,
          it is defined over a set of trials, and can not be calculated
          for any individual trial (like coherence, or PLV)?</div>
        <div><br>
        </div>
        <div>Just quickly reading through "The pairwise phase
          consistency: A bias-free measure of rhythmic neuronal
          synchronization" (Vinck et al., 2010), this seems to be the
          case.</div>
        <div><br>
        </div>
        <div>Hope this helps,</div>
        <div>roey</div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Thu, Sep 18, 2014 at 3:30 PM, Hwee
          Ling Lee <span dir="ltr"><<a href="mailto:hweeling.lee@gmail.com" target="_blank">hweeling.lee@gmail.com</a>></span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div dir="ltr">
                <div>Dear all,</div>
                <div><br>
                </div>
                <div>I've got a question regarding extracting pairwise
                  phase consistency of individual trials for each
                  subject.</div>
                <div><br>
                </div>
                <div>Using the connectivity analyses tutorial as a
                  reference, I extracted the PPC using the fourier
                  information from the mtmfft (dpss taper).</div>
                <div><br>
                </div>
                <div>Here's an example of my code:</div>
                <div><br>
                </div>
                <div>
                  <div>    cfg                 = [];</div>
                  <div>    cfg.output          = 'fourier';</div>
                  <div>    cfg.channel         = {'all'};</div>
                  <div>    cfg.method          = 'mtmfft';</div>
                  <div>    cfg.keeptrials      = 'yes';</div>
                  <div>    cfg.tapsmofrq       = 5;</div>
                  <div>    </div>
                  <div>    % find the index for the c200 condition</div>
                  <div>    pre_c200_idx = find(data8.trialinfo == 200);</div>
                  <div>    </div>
                  <div>    cfg.trials          = pre_c200_idx;</div>
                  <div>    cfg.foilim          = [0 100]; % either the
                    full range of frequencies (data2.hdr.Fs/2) or up to
                    100 Hz</div>
                  <div>    cfg.taper           = 'dpss';</div>
                  <div>    HLF_pre_c200        = ft_freqanalysis(cfg,
                    data8);</div>
                </div>
                <div><br>
                </div>
                <div>The PPC is extracted using this code:</div>
                <div><br>
                </div>
                <div>
                  <div>    cfg                 = [];</div>
                  <div>    cfg.trials          = 'all';</div>
                  <div>    cfg.keeptrials      = 'yes';</div>
                  <div>    cfg.channel         = {'all'};</div>
                  <div>    cfg.removemean      = 'yes';</div>
                  <div>    </div>
                  <div>    cfg.method           = 'wppc';</div>
                  <div>    cfg.channelcmb       = {cfg.channel,
                    cfg.channel};</div>
                  <div>    </div>
                  <div>    HLF_pre_c200wppc      =
                    ft_connectivityanalysis(cfg, HLF_pre_c200);</div>
                </div>
                <div><br>
                </div>
                <div>Although I've specified to keep individual trials,
                  my output is still a 'chan_freq' dimord variable. It
                  does not contain any individual trial PPC information.
                  Is there a way to extract the connectivity for
                  individual trials?</div>
                <div><br>
                </div>
                <div>Thanks.</div>
                <div><br>
                </div>
                <div>Cheers,</div>
                <div>Hweeling</div>
                <div><br>
                </div>
              </div>
            </div>
            <br>
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          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      <pre>_______________________________________________
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    </blockquote>
    <br>
    <br>
    </div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">-- 
Dr. Tobias Staudigl
Fachbereich Psychologie - ZPR
Postfach ZPR
78457 Konstanz
ZPR, Haus 12
Tel.: <a href="tel:%2B49%20%280%297531%20%2F%2088%20-%205703" value="+497531885703" target="_blank">+49 (0)7531 / 88 - 5703</a>
</pre>
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<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">=================================================<br>Dr. rer. nat. Lee, Hwee Ling<br>Postdoc<br>German Center for Neurodegenerative Diseases (DZNE) Bonn<br><br>Email 1: hwee-ling.lee<at><a href="http://dzne.de/" target="_blank">dzne.de</a><br>Email 2: hweeling.lee<at><a href="http://gmail.com/" target="_blank">gmail.com</a><div><br></div><div><a href="https://sites.google.com/site/hweelinglee/home" target="_blank">https://sites.google.com/site/hweelinglee/home</a><br><br>Correspondence Address:<br>Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany<br>=================================================<br></div></div>
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