<div dir="ltr">Dear Eelke,<div><br></div><div>thank you for your response. </div><div><br></div><div>Here is my full preprocessing for one subject:</div><div><br></div><div>%%%%%%%%%%%%%%%</div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg = []</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.dataset <span class="gmail-Apple-converted-space"> </span>= [myTMSEEGs(numSubj).SinglePulse.(curSubjSP{SPnum}).filepath <span class="gmail-s1" style="color:rgb(178,69,243)">'/'</span> myTMSEEGs(numSubj).SinglePulse.(curSubjSP{SPnum}).filename];</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">EEG <span class="gmail-Apple-converted-space"> </span>= pop_loadset(<span class="gmail-s1" style="color:rgb(178,69,243)">'filename'</span>, myTMSEEGs(numSubj).SinglePulse.(curSubjSP{SPnum}).filename, <span class="gmail-s1" style="color:rgb(178,69,243)">'filepath'</span>, [myTMSEEGs(numSubj).SinglePulse.(curSubjSP{SPnum}).filepath <span class="gmail-s1" style="color:rgb(178,69,243)">'/'</span>]);</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">% adding trialdef information to configuration file</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.trialdef.eventtype<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s1" style="color:rgb(178,69,243)">'trigger'</span>;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.trialdef.eventvalue <span class="gmail-Apple-converted-space"> </span>= 128; <span class="gmail-s2" style="color:rgb(37,153,45)">% TMS trigger</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.trialdef.prestim<span class="gmail-Apple-converted-space"> </span>= 1;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.trialdef.poststim <span class="gmail-Apple-converted-space"> </span>= 1;</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">% defining trial</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg <span class="gmail-Apple-converted-space"> </span>= ft_definetrial(cfg);</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">% freq analysis prep</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">dataSP<span class="gmail-Apple-converted-space"> </span>= eeglab2fieldtrip(EEG, <span class="gmail-s1" style="color:rgb(178,69,243)">'preprocessing'</span>);</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">dataSP.cfg<span class="gmail-Apple-converted-space"> </span>= cfg;</p>
<p class="gmail-p4" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45);min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">% interpolating NaN values before frequency analysis</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg <span class="gmail-Apple-converted-space"> </span>= [];</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.prewindow <span class="gmail-Apple-converted-space"> </span>= 0.995; <span class="gmail-s2" style="color:rgb(37,153,45)">% -5 ms</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.postwindow<span class="gmail-Apple-converted-space"> </span>= 0.990; <span class="gmail-s2" style="color:rgb(37,153,45)">% 10 ms</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.method<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s1" style="color:rgb(178,69,243)">'linear'</span>;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">dataSP<span class="gmail-Apple-converted-space"> </span>= ft_interpolatenan(cfg, dataSP);</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">% frequency analysis</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg <span class="gmail-Apple-converted-space"> </span>= [];</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.output<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s1" style="color:rgb(178,69,243)">'powandcsd'</span>;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.method<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s1" style="color:rgb(178,69,243)">'mtmconvol'</span>;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.foi <span class="gmail-Apple-converted-space"> </span>= 2:1:40;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)"><span class="gmail-s3" style="color:rgb(0,0,0)">cfg.t_ftimwin <span class="gmail-Apple-converted-space"> </span>=<span class="gmail-Apple-converted-space"> </span>2 ./ cfg.foi; </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)"><span class="gmail-s3" style="color:rgb(0,0,0)">cfg.tapsmofrq <span class="gmail-Apple-converted-space"> </span>= 0.4 *cfg.foi; </span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.toi <span class="gmail-Apple-converted-space"> </span>= -0.4:0.01:0.4;</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">dataSPfreq = ft_freqanalysis(cfg, dataSP);</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)">%baseline correction</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg = [];</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.baseline = [-0.4 -0.1];</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.baselinetype = <span class="gmail-s1" style="color:rgb(178,69,243)">'db'</span>;</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">dataSPfreq_bl = ft_freqbaseline(cfg, dataSPfreq);</p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier"><br></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font size="2" style="" face="arial, helvetica, sans-serif">%%%%%%%%%%%%%%%%%%%%%%%%</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier"><br></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">I tried a few things as you suggested:</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2"><br></font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">1. my ft_freqanalysis is only outputting positive values (variable dataSPfreq) and baseline db correction has both positive and negatives (as to be expected)</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">2. the error was the same between powandcsd</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2"><br></font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">3. I believe the mistake is related to calling for the baseline normalization a second time (cfg.baseline = [-0.4 -0.1] and cfg.baselinetype = 'db'). Once removing these configurations, I was able to use singleplotTFR fine. Would this produce the errors reported earlier?</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2"><br></font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">Finally, if the error was related to the aforementioned seconding calling of baseline normalization, and assuming removing it is the correct solution, is it best to perform a baseline normalization following ft_freqanalysis if the goal is to eventually move onto group-differences using the permutation method?</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2"><br></font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">Thank you again for your help.</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;line-height:normal"><font face="arial, helvetica, sans-serif" size="2">Paul</font></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier"><br></p></div></div>