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Hi Alex,
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<div class="">If this is the code you used:</div>
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<div class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg = [];</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.output = 'pow';</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.channel = 'Cz';</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.method = 'mtmconvol'; </span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.taper = 'hanning'; </span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.foi = 1:0.025:30; % OR 4:0.025:30</span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.t_ftimwin = 3./cfg.foi; </span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">cfg.toi = -0.5:0.01:0.7; </span><br style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;" class="">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">TFRwave = ft_freqanalysis(cfg, trialdata);</span></div>
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</span></font></div>
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</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span style="background-color: rgb(255, 255, 255);" class="">There shouldn’t be a difference in the values from 4 - 30 Hz, whether, or not you calculate 1-4 Hz as well. The NaN
values for the lower frequencies at the edges (and for very low frequencies for the entire time course) can be explained by the fact that your epochs from -1s to +1.2 are not long enough to fit even a single time window you are requesting. For example, in
cfg.t_ftimwin you are requesting a moving time window of 3 cycles. At 1 Hz (=oscillation with period of 1 second), you are requesting a 3 second moving time window. As your data is shorter than 3 seconds, you will not be able to estimate power at any of the
requested time points in cfg.toi. With an epoch length of 2.2 seconds you will only start to get estimates from ~1.4 Hz ( cycles/epoch length ) onwards.</span></font></div>
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<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span style="background-color: rgb(255, 255, 255);" class="">Best,</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class="">
</span></font></div>
<div class=""><font face="Calibri, Arial, Helvetica, sans-serif" size="3" class=""><span style="background-color: rgb(255, 255, 255);" class="">Jim</span></font></div>
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<div>
<blockquote type="cite" class="">
<div class="">On 1 Aug 2017, at 13:28, Alexander Mentink <<a href="mailto:amentink@chdr.nl" class="">amentink@chdr.nl</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks Jim,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">The graphs look a bit better, however I still get many NaN artifacts when I want to show the frequency range of 1-30 Hz, which disappears completely when I shift it to 4-30 Hz. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Does anyone know what the underlying problem is here?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">KR,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Alex</div>
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</font><font style="font-family: Verdana; font-size: 12pt; font-weight: bold;" class="">Alexander Mentink</font> <br class="">
<font face="Verdana" class="">Centre for Human Drug Research<br class="">
Zernikedreef 8<br class="">
2333 CL Leiden<br class="">
The Netherlands</font><font style="font-family: Verdana; font-size: 12pt;" class=""><br class="">
T +31 (0) 71 7517166</font><br class="">
<font style="font-family: Verdana; font-size: 12pt;" class=""><a href="mailto:amentink@chdr.nl" class="">amentink@chdr.nl</a></font><br class="">
<font face="Verdana" class=""><a href="http://www.chdr.nl/" class="">http://www.chdr.nl</a><br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>
<<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> on behalf of Herring, J.D. (Jim) <<a href="mailto:J.Herring@donders.ru.nl" class="">J.Herring@donders.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>01 August 2017 13:05<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Time frequency analysis using evoked potentials</font>
<div class=""> </div>
</div>
<div class="">Dear Alex,
<div class=""><br class="">
</div>
<div class="">Change your scaling to ‘maxabs’ (cfg.zlim = ‘maxabs’;) to get a better feel of the scaling of your data. Now you have a scaling from 0 to 1, which, given your data, gives you very saturated images. </div>
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</div>
<div class="">Also, I would argue using a relative baseline on a TFR of an ERP (or ERF) is risky as in theory, your baseline should be zero (you even explicitly try to impose that by performing a baseline correction when calculating the ERP). This means that
you are dividing your activation period by values close to zero. This will give you arbitrarily large values. An absolute baseline is preferred. </div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Jim</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 1 Aug 2017, at 11:52, Alexander Mentink <<a href="mailto:amentink@chdr.nl" class="">amentink@chdr.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi Fieldtrip community,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am trying to analyse time frequency representations of electrical evoked potentials, but I am not getting any reliable results at all.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Using hanning window (1-30 Hz) or (4-30 Hz), wavelet transform with absolute baselinetype and relative baselinetype gives me four totally different results (see link)</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><a href="http://tinyurl.com/y7nerh8v" id="LPlnk953677" class="">http://tinyurl.com/y7nerh8v</a><br class="">
<br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">The EEG data is defined 1000 ms pre stimulus and 1200 ms post stimulus, artifacts removed and preprocessed with baseline correction between 200 ms and 0 ms, bandpass filtered between 0.5 - 30 Hz and
referenced to earlobes. The timelocked analysis is attached to the dropbox link as well.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class="">The code I use for hanning window is</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">%%%%%%%%%%%%%%%%%%</div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="">cfg = [];<br class="">
cfg.output = 'pow';<br class="">
cfg.channel = 'Cz';<br class="">
cfg.method = 'mtmconvol'; <br class="">
cfg.taper = 'hanning'; <br class="">
cfg.foi = 1:0.025:30; % OR 4:0.025:30<br class="">
cfg.t_ftimwin = 3./cfg.foi; <br class="">
cfg.toi = -0.5:0.01:0.7; <br class="">
TFRwave = ft_freqanalysis(cfg, trialdata);<br class="">
<br class="">
</div>
<div class="">% Visualization<br class="">
cfg = [];<br class="">
cfg.baseline = [-0.5 -0.1]; <br class="">
cfg.baselinetype = 'absolute'; <br class="">
cfg.maskstyle = 'saturation';<br class="">
cfg.zlim = [0 1];<br class="">
cfg.showlabels = 'yes'; <br class="">
figure<br class="">
ft_singleplotTFR(cfg, TFRwave)</div>
<div class=""><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;">%%%%%%%%%%%%%%%%%%</span><br class="">
</div>
<div class=""><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;"><br class="">
</span></div>
<div class=""><b class="">And for wavelet transform is</b></div>
<div class=""><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;">%%%%%%%%%%%%%%%%%%</span><br class="">
</div>
<div class="">
<div class="">cfg = [];</div>
<div class="">cfg.channel = 'Cz';<span class="" style="white-space: pre;"> </span>
<span class="Apple-converted-space"> </span> </div>
<div class="">cfg.method = 'wavelet'; </div>
<div class="">cfg.width = 7; </div>
<div class="">cfg.output = 'pow';<span class="" style="white-space: pre;"> </span>
</div>
<div class="">cfg.foi = 1:0.5:30;<span class="" style="white-space: pre;">
</span><span class="Apple-converted-space"> </span> </div>
<div class="">cfg.toi = -0.5:0.05:1;<span class="" style="white-space: pre;">
</span></div>
<div class="">TFRwave = ft_freqanalysis(cfg, trialdata);</div>
<div class=""><br class="">
</div>
<div class=""><span class="" style="font-size: 12pt;">cfg = [];</span><br class="">
</div>
<div class="">cfg.baseline = [-0.5 -0.1]; </div>
<div class="">cfg.baselinetype = 'relative'; % OR absolute</div>
<div class="">cfg.maskstyle = 'saturation';<span class="" style="white-space: pre;">
</span></div>
<div class="">cfg.zlim = [0 1];<span class="" style="white-space: pre;"> </span>
</div>
<div class="">cfg.channel = 'Cz';</div>
<div class=""><span class="" style="font-size: 12pt;">figure</span><br class="">
</div>
<div class="">ft_singleplotTFR(cfg, TFRwave);</div>
<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;">%%%%%%%%%%%%%%%%%%</span><br class="">
</div>
<div class=""><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;"><br class="">
</span></div>
<div class="">I have tried the tutorials online, but this doesn't give me any better results...</div>
<div class=""><br class="">
</div>
<div class="">Does anyone know what I am doing wrong?</div>
<div class=""><br class="">
</div>
<div class="">Thanks many times!</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class=""><br class="">
</div>
<div class="">Alex (Master student </div>
<br class="">
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<td class="" style="width: 354px;"><font face="Verdana" class=""><br class="">
</font><font class="" style="font-family: Verdana; font-size: 12pt; font-weight: bold;">Alexander Mentink</font> <br class="">
<font face="Verdana" class="">Centre for Human Drug Research<br class="">
Zernikedreef 8<br class="">
2333 CL Leiden<br class="">
The Netherlands</font><font class="" style="font-family: Verdana; font-size: 12pt;"><br class="">
T +31 (0) 71 7517166</font><br class="">
<font class="" style="font-family: Verdana; font-size: 12pt;"><a href="mailto:amentink@chdr.nl" class="">amentink@chdr.nl</a></font><br class="">
<font face="Verdana" class=""><a href="http://www.chdr.nl/" class="">http://www.chdr.nl</a><br class="">
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<font face="Verdana" style="font-size: 12px; 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;" class=""></font><span style="font-family: Helvetica; font-size: 12px; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; 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;" class="">
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mailing list</span><br style="font-family: Helvetica; font-size: 12px; 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;" class="">
<a href="mailto:fieldtrip@donders.ru.nl" style="font-family: Helvetica; font-size: 12px; 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="">fieldtrip@donders.ru.nl</a><br style="font-family: Helvetica; font-size: 12px; 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;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 12px; 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></div>
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