<div dir="ltr"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">thanks Jan Mathijs for your reply, yes not to blame for not finishing up ... a lot of nice work already in his paper!</span><div><span style="text-align:start;text-indent:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="font-size:12.8px"><br></span></span></div><div><span style="text-align:start;text-indent:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="font-size:12.8px">after reading your tutorial (<a href="http://www.fieldtriptoolbox.org/project/guidelines/paper/connectivity_analysis?s[]=coherence&s[]=lags">http://www.fieldtriptoolbox.org/project/guidelines/paper/connectivity_analysis?s[]=coherence&s[]=lags</a>) still would love your thoughts on this.</span><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">ideally, I<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">'d like to find out whether a specific phase of an </span>ultraslow (<0.5Hz rhythmic external) signal is leading/lagging the phase of the iEEG signal at the same frequency (effective connectivity). <span style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Would it be adequate here to use<span style="font-family:arial,sans-serif;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;color:rgb(0,0,0);font-size:12.8px"> '</span><span style="font-family:arial,sans-serif;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;color:rgb(0,0,0);font-size:12.8px">granger' over 'pdc' since I'm not interested in the freq domain (as both signals have been filtered <0.5Hz). Note that<span style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"> dominant frequencies<span> </span></span><span style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;background-color:rgb(255,255,255);float:none;display:inline">between signals </span><span style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">differs a lot.</span></span></span></span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Also, interesting to know if there are consistent phase lags in some iEEG electrodes but not others <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">(functional</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"> connectivity</span><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">)</span>. which ft measures would you advice particularly if you want to compute phase lags? The Nolte (2004) paper suggested </span></span><span style="color:rgb(0,0,0);font-size:12.8px">cfg.method = 'coh' & cfg.complex = 'imag' as being a superior method. Is that right for this particular case? Would it be adequate here to use cfg.method='</span><span style="color:rgb(0,0,0);font-size:12.8px">wpli'  or 'wpli_debiased' </span><span style="color:rgb(0,0,0);font-size:12.8px">? I've explored other methods (Guo, 2007, PLoS) but not sure they're adequate for this specific case (where dominant frequencies <span style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">between signals </span>differs a lot).</span></div><div><span style="color:rgb(0,0,0);font-size:12.8px"><br></span></div><div><span style="color:rgb(0,0,0);font-size:12.8px">thanks</span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 17, 2018 at 3:26 AM, Schoffelen, J.M. (Jan Mathijs) <span dir="ltr"><<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



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Dear Jose,
<div>As far as I know, this code is not functional. The first author of the paper started the implementation in fieldtrip-style, but never finished it.</div>
<div>Also, note that the method itself is not strictly speaking a ‘connectivity’ measure, but it was intended to identify rhythmicity within signals.</div>
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<div>Best wishes,</div>
<div>Jan Mathijs</div>
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J.M.Schoffelen, MD PhD<br>
Associate PI, VIDI-fellow<br>
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br>
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<blockquote type="cite"><div><div class="h5">
<div>On 16 May 2018, at 18:17, Jose Herrero <<a href="mailto:jose.herrero66@gmail.com" target="_blank">jose.herrero66@gmail.com</a>> wrote:</div>
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<div><font face="times new roman, serif">dear Fieldtrippers,</font></div>
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<div><font face="times new roman, serif">I'm comparing different coherence methods including the fieldtrip method of lagged coherence. </font></div>
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<div><font face="times new roman, serif">running the code with...</font></div>
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<font color="#ff0000" face="times new roman, serif">cfg.method<span class="m_-5840453746741047528gmail-Apple-converted-space">     
</span>= <span class="m_-5840453746741047528gmail-s1">'laggedcoherence'</span>;</font></div>
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<font color="#ff0000" face="times new roman, serif">lcoh                 = ft_connectivityanalysis(cfg, freq)</font></div>
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<font face="times new roman, serif">results on...<br>
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<font color="#ff0000" face="times new roman, serif">Error using ft_connectivityanalysis (line 375)</font></div>
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<font color="#ff0000" face="times new roman, serif">unknown method laggedcoherence</font></div>
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<div><span style="color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><font face="times new roman, serif"><br>
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<div><font face="times new roman, serif"><span style="color:rgb(34,34,34);font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">running
 the code with...</span><br>
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<font color="#ff0000" face="times new roman, serif">lcoh = ft_connectivity_<wbr>laggedcoherence(cfg, freq)</font></div>
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<font face="times new roman, serif">results on: <br>
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<div><font color="#ff0000" face="times new roman, serif">In an assignment  A(:) = B, the number of elements in A and B must be the same.</font></div>
<div><font face="times new roman, serif"><span style="color:rgb(255,0,0)">Error in ft_connectivity_<wbr>laggedcoherence (line 213)</span><br>
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<div><font color="#ff0000" face="times new roman, serif">      lagwidth(lagindx) = cfg.lag*cyclelength*lagindx;</font></div>
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<div><font face="times new roman, serif">as 'cfg.lag' is assigned a length equal to the length of the trial (1x15000, single trial).</font></div>
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<div><font face="times new roman, serif">if this method works, is it possible to use it to compute lagged coherence between an external signal (which oscillates at a freq <0.5Hz) and the iEEG brain signal?</font></div>
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<div><font face="times new roman, serif">thanks,</font></div>
<div><font face="times new roman, serif">JHerr</font></div>
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______________________________<wbr>_________________<br>
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<br>______________________________<wbr>_________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div>Jose L Herrero, PhD</div><div>Department of Neurosurgery</div><div><div>Northwell University Hospital</div></div><div>Feinstein Institute for Medical Research</div><div>New York</div><div><br></div></div></div></div></div></div>
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