<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Danielle,<div><br></div><div>your problem is probably that you are feeding continuous data to the newcrossf function. This type of coherence is only defined when you have multiple trials. As in another recent message, you may read the article below (and more specifically look for ERPCOH, page 9)</div><div><br></div><div>Delorme, A., Makeig, S. (2004) EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. <i>Journal of Neuroscience Methods</i>, 134(1), 9-21. <a href="http://sccn.ucsd.edu/%7Earno/mypapers/eeglab_jnm03.pdf"><span class="s2">Author's PDF</span></a>, <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T04-4BM8KF5-1&_user=4429&_handle=W-WA-A-A-AB-MsSAYZA-UUW-AUDDUYUYBC-WVDBUDUBY-AB-U&_fmt=full&_coverDate=03%2F15%2F2004&_rdoc=2&_orig=browse&_srch=%23toc%234852%232004%23998659998%23480525%21&_cdi=4852&view=c&_acct=C000000152&_version=1&_urlVersion=0&_userid=4429&md5=668ee0cf28c68cd60f155239a2d7d023"><span class="s2">Science direct</span></a>.</div><div><br></div><div>Best, </div><div><br></div><div>Arno</div><div><br><div><div>On Jul 11, 2011, at 11:15 AM, Danielle Farrar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello everyone,<div><br></div><div>I'm trying to use the crossf function to get values for the coherence across channels at different frequencies. I'm having trouble with the documentation of the function -- when I type help crossf into the matlab command line, it says that the output is as follows:</div>
<div><br></div><div><div>Outputs: </div><div> coh = Matrix (nfreqs,timesout) of coherence magnitudes </div><div> mcoh = Vector of mean baseline coherence at each frequency</div><div> timesout = Vector of output latencies (window centers) (ms).</div>
<div> freqsout = Vector of frequency bin centers (Hz).</div><div> cohboot = Matrix (nfreqs,2) of [lower;upper] coher signif. limits</div><div> if 'boottype' is 'trials', (nfreqs,timesout, 2)</div>
<div> cohangle = (nfreqs,timesout) matrix of coherence angles (in radians)</div><div> cohangles = (nfreqs,timesout,trials) matrix of single-trial coherence </div><div> angles (in radians), saved and output only if 'savecoher',1</div>
</div><div><br></div><div>What I am trying to do is average some evoked potential data, and then compare pair-wise, a series of the electrodes to determine their coherence, which I will eventually write to a file. I am new to this, so am having trouble understanding how to interpret the output of the crossf function, which I assume will give me what I am looking for. </div>
<div><br></div><div>So my questions is: the first output matrix that I get produces a 1.0 for every cell in the matrix for the electrodes I've tried -- is it likely that they are that in sync? That should be giving me the matrix of coherence magnitudes, correct? How is the coherence calculated? I also print out the mean baseline coherence, which also gives a matrix of 1s.</div>
<div><br></div><div>Here is a sample of the code I am trying to use (I am aware that the loops will only be executed once, this is for debugging purposes):</div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><span class="s1"><b>for </b></span><b>i=9:9,</b></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p2"><b> EEG = eeg_checkset( EEG );</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(i);</b></p>
</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(channels{i});</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p2"><b> erp = pop_erpimage(EEG,1, [i],[],wcst_rare,0,1,{},[],<span class="s2">''</span> , <span class="s2">'yerplabel'</span>, <span class="s2">'\muV'</span>, <span class="s2">'erp'</span>, <span class="s2">'on'</span>, <span class="s2">'limits'</span>,[NaN NaN -25 25 NaN NaN NaN NaN] , <span class="s2">'cbar'</span>, <span class="s2">'on'</span>, <span class="s2">'vert'</span>,[170 300] );</b></p>
</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> erp_avg = mean(erp,2);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p1"><b> </b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> <span class="s1">for</span> j=14:14,</b></p>
</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> erp2 = pop_erpimage(EEG,1, [j],[],wcst_rare,0,1,{},[],<span class="s2">''</span> , <span class="s2">'yerplabel'</span>, <span class="s2">'\muV'</span>, <span class="s2">'erp'</span>, <span class="s2">'on'</span>, <span class="s2">'limits'</span>,[NaN NaN -25 25 NaN NaN NaN NaN] , <span class="s2">'cbar'</span>, <span class="s2">'on'</span>, <span class="s2">'vert'</span>,[170 300] );</b></p>
</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> erp_avg2 = mean(erp2,2);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p2"><b> [R, mbase, times, freqs]= crossf(erp_avg,erp_avg2,1150,[-150 999],1000,0,<span class="s2">'type'</span>,<span class="s2">'coher'</span>);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p3"><span class="s3"><b> disp(</b></span></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>'Displaying coherence values'<span class="s3">);</span></b></div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(R);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p3"><span class="s3"><b> disp(</b></span></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>'Displaying mean baseline coherence values'<span class="s3">);</span></b></div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(mbase);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p3"><span class="s3"><b> disp(</b></span></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>'Displaying times'<span class="s3">);</span></b></div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(times);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p3"><span class="s3"><b> disp(</b></span></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>'Displaying freqs'<span class="s3">);</span></b></div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> disp(freqs);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p2"><b> disp(<span class="s2">'Size of times'</span>);</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2">
<b> disp(size(times));</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p3"><span class="s3"><b> disp(</b></span></p>
</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>'Size of freqs'<span class="s3">);</span></b></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div><p class="p2"><b> disp(size(freqs));</b></p></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p2"><b> <span class="s1">end</span></b></p>
</div></blockquote></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="p1"><b>end</b></p></div></blockquote>
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