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<p>Dear Stephen, <br>
</p>
<p><br>
</p>
<p>thanks a lot for your reply.<br>
</p>
<p>I actually figured out the baseline was the issue, as I was computing the Morlet on a shorter time-window and I was trying to baseline-correct with an interval that was outside of my TFR. With this adjustment I do see the plot as I expected it.<br>
</p>
<p><br>
</p>
<p>Concerning the warning on the cfg.toi, I chose on purpose the step according to my sampling rate, but I will consider increasing it. My concern is that I might somehow be losing information due to this mismatch between input and output time-bins.<br>
</p>
<p><br>
</p>
<p>Thanks!<br>
</p>
<p>Best,<br>
</p>
<p>Silvia<br>
</p>
<div style="color: rgb(33, 33, 33);">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br>
<b>Sent:</b> 26 July 2018 11:32<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] ft_freqanalysis wavelet problem</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear Silvia,<br>
<br>
The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information,
speeding it up as well)<br>
<br>
Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You
might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options.<br>
<br>
Best wishes,<br>
Stephen</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 July 2018 at 09:57, Silvia Formica <span dir="ltr">
<<a href="mailto:Silvia.Formica@ugent.be" target="_blank">Silvia.Formica@ugent.be</a>></span> wrote:<br>
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<p>Dear all, <br>
</p>
<p><br>
</p>
<p>I am new to fieldtrip so I apologize in advance if my question is trivial.<br>
</p>
<p>I am trying to run a time frequency analysis with Morlet wavelets. </p>
<p>Here is the code I am using:<br>
</p>
<p><br>
</p>
<div>cfg = [];</div>
<div>cfg.channel = 1:64;<span style="white-space:pre-wrap"> </span> <br>
</div>
<div>cfg.method = 'wavelet'; </div>
<div><span style="font-size:12pt">cfg.pad = 10;</span><br>
</div>
<div><span style="font-size:12pt">cfg.width = 7; </span><br>
</div>
<div>cfg.output = 'pow';<span style="white-space:pre-wrap"> </span></div>
<div>cfg.foi = 4:1:30;<span style="white-space:pre-wrap"> </span> </div>
<div>cfg.toi = 0:0.0039:2;<span style="white-space:pre-wrap"> </span> % my sampling rate is 512 Hz </div>
<div>TFRwave = ft_freqanalysis(cfg, data_clean);<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Where data_clean is the struct containing my trials. <span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">All my trials are the same length.</span><br>
</div>
<div><br>
</div>
<div>When I run this code, I get the following warning:<br>
</div>
<div><br>
</div>
<div>
<div>Warning: output time-bins are different from input time-bins </div>
<div>trial 1, frequency 26 (29.00 Hz)</div>
<div>Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz)<br>
</div>
<div>
<div>Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz)</div>
<div>Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz)<br>
</div>
<div>Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz)<br>
</div>
</div>
<div>[...]<br>
</div>
<div><br>
</div>
<div>I have no idea what this means. Any suggestion?<br>
</div>
<div><br>
</div>
<div>Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot:<br>
<br>
</div>
<div>
<div>cfg = [];</div>
<div>cfg.baseline = [-0.5 -0.1]; </div>
<div>cfg.baselinetype = 'absolute'; <span style="white-space:pre-wrap"></span> </div>
<div>cfg.zlim = [-3e-27 3e-27];<br>
</div>
<div>cfg.showlabels = 'yes';<span style="white-space:pre-wrap"> </span> </div>
<div>cfg.layout = 'biosemi64.lay';</div>
<div>figure</div>
<div>ft_multiplotTFR(cfg, TFRwave)<br>
<br>
</div>
<div><br>
</div>
<div>When I check the content of my TFRwave I can see it is not made of NaNs. </div>
<div>Is the problem due to the setting cfg.zlim? It is not clear to me how to set it.<br>
</div>
<div><br>
</div>
<div>Thanks in advance for any help!<span class="HOEnZb"><font color="#888888"><br>
</font></span></div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Silvia<br>
</div>
</font></span></div>
<br>
</div>
<div><br>
</div>
<p><br>
</p>
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<br>
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</blockquote>
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