Hi all,<div>Ian Gould, the author of the paper I cited in my previous mail, also replied to me. He kindly asked me to post his reply on the mailing list.</div><div><br></div><div>Thanks again for your help</div><div><br></div>
<div>Silvia</div><div><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Ian Gould</b> <span dir="ltr"><<a href="mailto:ian.gould@psy.ox.ac.uk">ian.gould@psy.ox.ac.uk</a>></span><br>
Date: Tue, Jun 26, 2012 at 6:57 PM<br>Subject: FW: [FieldTrip] multitaper and NaN<br>To: "Pagano, Silvia" <<a href="mailto:silvia.pagano@unitn.it">silvia.pagano@unitn.it</a>><br><br><br>
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Hi Silvia,</div>
<div><br>
</div>
<div>Although I'm not subscribed to it at the moment, a friend of mine monitors the field trip email list and forwarded your question to me.</div>
<div><br>
</div>
<div>The boundary effects you are talking about occur because oscillatory signals have to be computed over a time window. The time window width is specified for each frequency you are analysing in cfg.t_ftimwin, and is centred on the time point you are trying
to compute power at. So, if the half-width of the window is greater than the distance from a time point to the edge of your data, field trip will not be able to compute power at that frequency. The solution to this is to (1) use a shorter time window, and/or
(2) calculate data over longer epochs so the boundary effect doesn't affect the time points you are interested in.</div>
<div><br>
</div>
<div>In the code you posted, the time window varies with frequency, unlike the fixed window we used in our JNeurophys paper. Your missing data at lower frequencies are explained by this. For example, you'd need 2.5s of data to estimate power at 2Hz with
your settings. To get 500ms smoothing you could use:</div>
<div>cfg.t_ftimwin = 0.5 *ones(1,length(cfg.foi));</div>
<div><br>
</div>
<div>Similarly, for 2Hz smoothing you'd want something like:</div>
<div>cfg.tapsmofrq = 2*ones(1,length(cfg.foi));</div>
<div>
<div><br>
</div>
<div>Finally, for 50ms steps you'd want:</div>
<div>cfg.toi = -1.1:0.05:0.1;</div>
</div>
<div><br>
</div>
<div>Hope that helps. Let me know if any other questions. Also, could you please post this to the list on my behalf, so others know that your question has been answered.</div>
<div><br>
</div>
<div>Kind Regards,</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div> </div>
<div>
<div><br>
</div>
</div>
<div><br>
</div>
<span>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Andre Cravo <<a href="mailto:andrecravo@gmail.com" target="_blank">andrecravo@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 26 June 2012 17:11<br>
<span style="font-weight:bold">To: </span>Ian Gould <<a href="mailto:ian.gould@psy.ox.ac.uk" target="_blank">ian.gould@psy.ox.ac.uk</a>>, "<a href="mailto:ian.gould@merton.ox.ac.uk" target="_blank">ian.gould@merton.ox.ac.uk</a>" <<a href="mailto:ian.gould@merton.ox.ac.uk" target="_blank">ian.gould@merton.ox.ac.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Fwd: [FieldTrip] multitaper and NaN<br>
</div>
<div><br>
</div>
<div>
<div>Hello Ian,<br>
<br>
How are you? I hope all is well.<br>
<br>
I'm pretty sure you get fieldtrip emails, but I saw this one and thought you might like to give a help.<br>
<br>
Cheers<br>
<br>
Andre<br>
<br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Silvia Pagano</b> <span dir="ltr"><<a href="mailto:silvia.pagano@unitn.it" target="_blank">silvia.pagano@unitn.it</a>></span><br>
Date: 26 June 2012 13:04<br>
Subject: [FieldTrip] multitaper and NaN<br>
To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>
<br>
<br>
Dear list subscribers,
<div><br>
</div>
<div>I am an ERPer looking for the first time into the world of time-frequency analysis. I am trying to perform some multitaper analysis on a data set. Ideally I would like to perform similar analysis as described in a paper by Gould et al (2011) on Journal
of Neurophysiology. (i.e. in their own words "Time-frequency analysis was performed on</div>
<div>all epochs using a multitaper approach (2–30 Hz, 0.5-Hz steps, 500-ms temporal smoothing window, 2-Hz frequency resolution)" )</div>
<div><br>
</div>
<div>I have epochs from -1100 ms to 100 time locked to the stimulus onset and I am trying to replicate the analysis they did. The problem is that I got boundary effects on all my conditions, namely I obtain NaN in the extreme 100 ms of the time window for all
frequencies and for very low frequencies (e.g. 2-4Hz) I have no data in the whole time window. I thought I had time windows large enough to avoid boundary effects, however there must be something I am missing in my code. </div>
<div><br>
</div>
<div>Here's what I did following the tutorial:</div>
<div><br>
</div>
<div>
<div>
<div>cfg = [];</div>
<div>cfg.output = 'pow';</div>
<div>cfg.channel = 'EEG';</div>
<div>cfg.method = 'mtmconvol'; </div>
<div>cfg.foi = 2:2:30;</div>
<div>cfg.t_ftimwin = 5./cfg.foi; </div>
<div>cfg.tapsmofrq = 0.4*cfg.foi;</div>
<div>cfg.toi = -1.1:0.02:0.1;</div>
<div>cfg.pad = 'maxperlen'; </div>
<div>TFRmult = ft_freqanalysis(cfg, data); </div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Does anyone have a clue on this?</div>
<div><br>
</div>
<div><br>
</div>
<div>Thank you very much</div>
<span><font color="#888888">
<div><br>
</div>
<div>Silvia</div>
-- <br>
__________________________________<br>
<br>
Silvia Pagano PhD student<br>
CIMeC - Center for Mind/Brain Science<br>
Corso Bettini, 31 38068 Rovereto (TN) <br>
Tel. <a href="tel:%2B39%200464%20808709" value="+390464808709" target="_blank">+39 0464 808709</a><br>
<br>
</font></span></div>
<br>
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</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<br clear="all">
<br>
-- <br>
<span>Andre M. Cravo<br>
<span style="color:rgb(102,102,102)">Postdoctoral Researcher</span><br style="color:rgb(102,102,102)">
<span style="color:rgb(102,102,102)">University of Sao Paulo-Brazil</span><br>
</span><br>
</font></span></div>
</div>
</span>
</div>
</div><br><br clear="all"><div><br></div>-- <br>__________________________________<br><br>Silvia Pagano PhD student<br>CIMeC - Center for Mind/Brain Science<br>Corso Bettini, 31 38068 Rovereto (TN) <br>Tel. +39 0464 808709<br>
<br>
</div>