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<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Mireia,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">I’ve been encountering a similar problem this week, where baselining after ft_freqanalysis with keeptrials = ‘yes’ gives unexpected results. I found this message from Jan-Mathijs Schoffelen
online: <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">“With keeptrials = 'yes', the baseline correction is applied to every single trial, with keeptrials = 'no', the baseline correction is only applied to the
average. Since the baseline operation that you have specified is the result of a division, this yields different results. In general, first averaging, then baseline correcting makes more sense.” (<a href="https://urldefense.com/v3/__https://github.com/fieldtrip/fieldtrip/issues/670__;!!HJOPV4FYYWzcc1jazlU!9ZMUVm3KHFhKEJIxX50B-SHHjYkPYFKdHS6dyDVryLWDQ1AUEhQnEy8RqjuGK2pChzi96-Dnja_fkfEYpkJHxLESXecWTuNeQu8p2w$">https://github.com/fieldtrip/fieldtrip/issues/670</a>)
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">So I think this would align with the fact that when you used a baseline that using division (db), you got the unexpected results, but not with the baseline that doesn’t involve division
(absolute). <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Jan-Mathijs mentions that in general first averaging makes more sense, but when you want to do single-trial analyses that’s of course not possible. In my case, I wanted to use ‘relchange’
to baseline, but doing so on the data with keeptrials = ‘yes’ shows a power increase in my crucial time window with respect to baseline, while doing so with keeptrials = ‘no’ shows a power decrease (as expected) (I’ve attached pictures for one participant
as an example). <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">I would be very curious to hear what baseline procedure people recommend for single-trial analyses!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Marlijn<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="en-NL"><a href="https://urldefense.com/v3/__https://www.mpi.nl/people/bekke-marlijn-ter__;!!HJOPV4FYYWzcc1jazlU!9ZMUVm3KHFhKEJIxX50B-SHHjYkPYFKdHS6dyDVryLWDQ1AUEhQnEy8RqjuGK2pChzi96-Dnja_fkfEYpkJHxLESXecWTuOqFZ44OA$"><b><span lang="en-NL" style="font-size:10.0pt;color:#404040;background:white;text-decoration:none">Marlijn ter Bekke</span></b></a></span><b><span style="font-size:10.0pt;color:#404040;background:white"><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#404040;background:white">PhD student @Donders Centre for Cognition</span><span lang="en-NL" style="font-size:10.0pt;color:#404040;background:white"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="en-NL" style="font-size:10.0pt;color:#404040;background:white">& Max Planck Institute for Psycholinguistics</span><span style="font-size:10.0pt;color:#404040;background:white"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="en-NL"><a href="https://urldefense.com/v3/__https://marlijn-ter-bekke.github.io/__;!!HJOPV4FYYWzcc1jazlU!9ZMUVm3KHFhKEJIxX50B-SHHjYkPYFKdHS6dyDVryLWDQ1AUEhQnEy8RqjuGK2pChzi96-Dnja_fkfEYpkJHxLESXecWTuNRHI8EnQ$"><span lang="en-NL" style="font-size:10.0pt;color:#404040">https://marlijn-ter-bekke.github.io/</span></a></span><span lang="en-NL" style="font-size:10.0pt;color:#404040">
</span><span style="font-size:10.0pt;color:#404040"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>TORRALBA CUELLO, MIREIA via fieldtrip<br>
<b>Sent:</b> Wednesday, 15 February 2023 17:15<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> TORRALBA CUELLO, MIREIA <mireia.torralba@upf.edu><br>
<b>Subject:</b> [FieldTrip] Single trial dB baseline correction<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">Dear FieldTrip community,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">I came across a problem when using dB baseline correction for single trial power-spectrum time courses. My problem is that all values turn to be negative, even in the baseline. When I averaged across trials and subjects,
to see if this was noise, I found that the values in the baseline were around -1 dB. I am using revision 20220104.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">When I inspected the function ft_freqbaseline, I came to see that the dB transformation is calculated after averaging the power in the temporal domain. That is:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">I calculate power spectrum:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">cfg=[];<br>
cfg.method='mtmconvol'; %STFT<br>
cfg.taper='hanning'; %Taper window used<br>
cfg.pad='nextpow2';<br>
cfg.foi=5:1:7; %Frequencies of interest (in Hz)<br>
cfg.toi=-0.5-0.24:0.05:1.5;<br>
cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);<br>
cfg.keeptrials='yes'; %We will inspect only the average power<br>
cfg.output='pow';<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">fdata=ft_freqanalysis(cfg,data);<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">In ft_freqbaseline:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">meanVals
</span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">=</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">
</span><span class="gmail-pl-en"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">repmat</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">(</span><span class="gmail-pl-en"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">nanmean</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">(</span><span class="gmail-pl-en"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">data</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">(</span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">:</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">,</span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">:</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">,<span class="gmail-pl-smi">baselineTimes</span>),
</span><span class="gmail-pl-c1"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">3</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">), [</span><span class="gmail-pl-c1"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">1</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">
</span><span class="gmail-pl-c1"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">1</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">
</span><span class="gmail-pl-en"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">size</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">(<span class="gmail-pl-smi">data</span>,
</span><span class="gmail-pl-c1"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">3</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">)]);</span><span lang="en-NL"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">Then, the dB transform is calculated as follows:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">data
</span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">=</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">
</span><span class="gmail-pl-c1"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">10</span></span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">*</span></span><span class="gmail-pl-en"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">log10</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">(<span class="gmail-pl-smi">data</span>
</span><span class="gmail-pl-k"><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas">./</span></span><span lang="en-NL" style="font-size:9.0pt;font-family:Consolas;color:#24292F">
<span class="gmail-pl-smi">meanVals</span>);</span><span lang="en-NL"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">As I mentioned, when I apply this procedure to my data using the following setting:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">cfg=[];<br>
cfg.baseline=[-0.5 0];<br>
cfg.baselinetype='db';<br>
fdata_baseline=ft_freqbaseline(cfg,fdata);<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"> I get very negative values in the baseline. However, if I first do the transform and then the baseline like this:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">cfg=[];<br>
cfg.operation='10*log10(x1)';<br>
cfg.parameter='powspctrm';<br>
fdata_log=ft_math(cfg,fdata);<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">cfg=[];<br>
cfg.baseline=[-0.5 0];<br>
cfg.baselinetype='absolute';<br>
fdata_baseline=ft_freqbaseline(cfg,fdata_log);<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">Taking advantage of the properties of the logarithm, then for trial and subject averaged data I obtain what I should expect, that the values in the baseline period are small and fluctuating around zero.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">I don't know, maybe the approach for calculating dB correction should be different for single and trial averaged power spectrum. Or maybe there was some error in my procedure.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">Thanks in advance,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="en-NL">Mireia<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888">Mireia Torralba Cuello<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888">Multisensory Research Group <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888">Center for Brain and Cognition, Universitat Pompeu Fabra<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888">Address: Edifici Mercè Rodoreda 24.313<br>
c\ Ramon Trias Fargas, 25-27<br>
08005 Barcelona</span><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="en-NL"><a href="https://urldefense.com/v3/__http:/www.mrg.upf.edu/__;!!HJOPV4FYYWzcc1jazlU!4sCV7xFJiK_VsVjZKxw5wNhPArLa1bmn6sjBfkf4XUH6MHmklClR3K21eGCks43NgrUUJ-t_-sYBqdsDMHjdgCs49R3n0Spy$" target="_blank"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1155CC">http://www.mrg.upf.edu</span></a></span><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span lang="en-NL" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#888888">Tel +34 935422745<o:p></o:p></span></p>
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