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Hi Daniel,
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<div class="">May I suggest you to do 4 things, rather than trying to really understand why no apparent baselining seems to have been applied.</div>
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<div class="">1 a). You can run ft_freqanalysis for all channels at once (without the for-loop)</div>
<div class="">1 b). You may want to use cfg.method = ‘wltconvol’ for ft_freqanalysis, rather than ‘wavelet’ , since it’s much faster with equivalent results.</div>
<div class="">2). Next, you can call ft_freqbaseline (again: only once, and perhaps use ‘relchange’ as a method) to ‘baseline correct' the spectrograms.</div>
<div class="">3). Next, you can use ft_multiplotTFR on the baseline corrected variable, using a cfg.layout = ‘ordered’, and don’t specify any baseline correction options here.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 18 Jun 2019, at 20:12, Daniel Campoy (CMP - Student) <<a href="mailto:D.Campoy@uea.ac.uk" class="">D.Campoy@uea.ac.uk</a>> wrote:</div>
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Hello,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I have been stuck trying to understand the results I’m seeing so please forgive me as my background is not in neuroscience. I’m a Masters student working with EEG data for a classification project using Matlab 2017b.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I have been successful at visualising the data of a test subject for a specific trigger and plot all channels (dataset has 8 channels) from the trigger (image stimuli) using ft_singleplotTFR. Thus creating a 2x4 plot of images for all 8 channels. However I’m
stuck trying understand my results when I plot an EEG spectrogram using ft_singleplotTFR for each channel across all triggers (T=1 in my dataset) the data does not show what I’ve seen for separate channels. It displays a plot of 8 images filled blue and a
fine yellow/green bar across the bottom. The only thing I’ve changed is supplying all the trials instead of one at a time using a for loop to iterate through each trial for 8 channels. I’ve removed the for loop outside of the for loop of channels since I’m
supplying all trials. Below is my code and process. Any insight would be much appreciated and if you need further information please let me know. I’ve attached an image of the results of each channel across all triggers.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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My first step is to load the .mat file I’ve saved containing all the defined trials. After this is complete, the below code is used to extract all the trigger events where the value in cfg.events is T=1. I run the ft_<span style="font-size: 10pt; font-family: "Courier New";" class="">preprocessing</span>again
but for the defined trials I’m looking for T=1.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">trigger = extractfield(cfg.event,</span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'value'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">);</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">channels = EEG_Data.cfg.channel;</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">trigger_idx = find(startsWith(trigger,</span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'T=1'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">));</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">cfg.trials = trigger_idx;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%index location for
all T=1 stimuli triggers</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">EEG_Data_Trial = ft_preprocessing(cfg,EEG_Data);<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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After completion the next block of code is ran for each channel. You may have noticed the cdat variable is in the output, this is me modifying the ft_singleplotTFR function to return the EEG spectrogram matrix I use for later analysis.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class="">figure<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%used to create a figure of EEG Spectrograms</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New"; color: blue;" class="">for</span><span style="font-size: 10pt; font-family: "Courier New";" class=""><span class="Apple-converted-space"> </span>z = 1:length(channels)<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%Collect
the measurements from each channel for a given trigger</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> Img_idx = 1 + Img_idx;</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg = [];</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.output =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'pow'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%return
power spectra</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.channel = channels{z};</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.method =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'wavelet'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%use
wavelet function</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%cfg.trials = trigger_idx;
%specify index location to find event in EEG_Data_Trial.trial</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.width = 1;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">% 3 has shown
some promise for results</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.gwidth = 4;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%decreasing
this has shown to fill out are of the figure</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.pad = 20;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%increases
resolution as the value goes up</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.foilim = [1 30];<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%1 to
30 Hz range</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> </span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%cfg.toi = -.10:0.0001:.35; %produced a full image time window from
-100 ms to 350ms in 0.1ms steps</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.toi = -.05:0.00001:.250;<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%time
window from -50 ms to 250ms in 0.01ms steps</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> </span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> TFRwavelet = ft_freqanalysis(cfg, EEG_Data_Trial);</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> fprintf(</span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'\n Time-Freq wavelet for trigger index %u channel %s and processed
%u trigger(s)\n'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">,trigger_idx(i),channels{z},i)</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%Create Image of EEG Spectrogram
to output cdat matrix</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg = [];</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.baselinetype =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'absolute'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">;</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.maskstyle =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'saturation'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">;</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> cfg.zlim = <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'maxmin'</span><span style="font-size: 10pt; font-family: "Courier New";" class="">;</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> subplot(2,4,z)</span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%used to create figures of plotted channels</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New";" class=""> [EEG_Spec,cdat] = ft_singleplotTFR(cfg, TFRwavelet);</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: "Courier New";" class=""> subplot(2,4,z)</span><span style="font-size: 10pt; font-family: "Courier New"; color: forestgreen;" class="">%used to create figures of plotted channels</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: "Courier New"; color: blue;" class="">end</span><span style="font-size: 12pt; font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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Thank you and kind regards,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Daniel C.<o:p class=""></o:p></div>
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<span id="cid:42B8D49E-6F92-4FCD-9031-55B2418CD8F4@dccn.nl"><OneSub_acrossTrails_T1.png></span><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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