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<p style="margin-top:0;margin-bottom:0">Hi Daniel,</p>
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<p style="margin-top:0;margin-bottom:0">I haven't been able to reproduce your problem exactly, but one point: Fieldtrip 'raw' data structures represent time in seconds. So if you are trying to create a data structure with 600 seconds of data, with a sampling
frequency of 1000Hz, then your time axis should go from 0 to 600 (or from n to 600+n).</p>
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<p style="margin-top:0;margin-bottom:0">So instead of</p>
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<p style="margin-top:0;margin-bottom:0"><span style="font-family: "Courier New", serif, "EmojiFont"; color: black;" lang="EN-GB">data.time{1} = 1:600000;</span></p>
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<p style="margin-top:0;margin-bottom:0">you should specify</p>
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<p style="margin-top:0;margin-bottom:0"><span style="font-family: "Courier New", serif, "EmojiFont"; color: black;" lang="EN-GB">data.time{1} = 0.001:0.001:600;</span></p>
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Good luck!</div>
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Best,</div>
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Tom<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of daniel.strahnen@uni-ulm.de <daniel.strahnen@uni-ulm.de><br>
<b>Sent:</b> 06 July 2019 15:23<br>
<b>To:</b> 'FieldTrip discussion list'<br>
<b>Subject:</b> [FieldTrip] Time-frequency granger analysis</font>
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<p class="x_MsoNormal">Dear FieldTrip – Community,</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal"><span lang="EN-GB">My goal is to analyse changes of Granger Causality over a certain time period.</span></p>
<p class="x_MsoNormal"><span lang="EN-GB">Here is the code I use to calculate the wavelet analysis:</span></p>
<p class="x_MsoNormal"><span lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">data.label = {</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH1'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH2'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH3'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH4'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH5'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH6'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'CH7'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">};</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">data.fsample = 1000;
</span><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">% Sampling rate of 1kH</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">data.time{1} = 1:600000;</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">data.trial{1} = Output_data';
</span><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">% Matrix organised as follows: 7 chan x 600000 samples</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">%% Wavelets for time-frequency power analysis</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg = [];</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg.output =
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'powandcsd'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg.method =
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'wavelet'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg.foi = 1:48;
</span><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">% Frequency range from 1 to 48Hz
</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5;
</span><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">% length of time window = 0.5 sec</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg.toi = 0:600;
</span><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">% 600 seconds (10min) time period</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">freq_data = ft_freqanalysis(cfg, data);</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB">Up to this point everything seems to be correct, but the granger analysis only gives my NaNs.</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:forestgreen" lang="EN-GB">%% Granger causality analysis</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg_conn = [];</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">cfg_conn.method =
</span><span style="font-family:"Courier New"; color:#A020F0" lang="EN-GB">'granger'</span><span style="font-family:"Courier New"; color:black" lang="EN-GB">;</span><span style="font-family:"Courier New"" lang="EN-GB"></span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB">granger_str = ft_connectivityanalysis(cfg_conn, freq_data);
</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="font-family:"Courier New"; color:black" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB">Does anyone has a suggestion what might be the mistake in my code?</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB">Thank you very much and best regards</span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB"> </span></p>
<p class="x_MsoNormal" style="text-autospace:none"><span style="color:black" lang="EN-GB">Daniel</span><span lang="EN-GB"></span></p>
<p class="x_MsoNormal"><span style="font-size:12.0pt" lang="EN-GB"> </span></p>
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