<div dir="ltr">Hey Benjy,<div><br></div><div>I would suspect this has to do with your (dft) filtering, which depends on the amount of data, and perhaps some small numerical differences due to resampling. Strange jumps at onset/offset of data segments also often indicate something to do with filtering.</div><div><br></div><div>To avoid this, and to create a fair comparison between your different trial duration segmentation, I would do the following:</div><div><br></div><div>- preprocess all your data as one long 'trial'. I.e. without segmentation. Do all your filtering at this step, i.e. at one go over all your data. This gives you the maximum frequency resolution & ability to filter low frequencies.</div><div>- segment your filtered data into trials using ft_redefinetrial.</div><div><div>- do your resampling </div><div></div></div><div>- check the different triallengths.</div><div><br></div><div>If anything stays slightly different, I would imagine it has to do with the resampling, because samples will end up slightly different on your axis, creating numerical differences. You could resample before segmenting, which would be more efficient, but then you'll have to deal with changing timing of your markers which would still be in the original samplerate. Dealing with time-axis and samples is a pain so personally I therefore always let FT deal with the resampling after trial segmentation.</div><div><br></div><div>Have fun,<br></div><div>Stephen</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Op di 2 feb. 2021 om 16:36 schreef Barnett, Benjy <<a href="mailto:benjy.barnett.20@ucl.ac.uk">benjy.barnett.20@ucl.ac.uk</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
<font face="Courier">Hey. When I am preprocessing my MEG neuromag data, I’m noticing that the signal of my channels are altered depending on how long after the stimulus I include in the trial, even in the portion of the trial that is overlapping between
the two cases. For instance, if I use cfg.poststim = 2.5 in one run and cfg.poststim = 0.6 in a second, the two signals are not identical up until 0.6 seconds. Please see my code and attached plots of a Grad sensor in these two cases up to 0.6 seconds.</font>
<div><font face="Courier"><br>
</font></div>
<div>
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)">
<font face="Courier"><span style="color:rgb(0,0,0)"><span style="white-space:pre-wrap"></span> </span>% define trials</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.dataset = full_path;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.trialdef.prestim = 0.175; </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.trialdef.poststim = 0.6;
<span style="color:rgb(34,139,34)">% compare with 2.5 seconds</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.trialdef.eventvalue = [6 7 9];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.trialdef.eventtype =
<span style="color:rgb(160,32,240)">'STI101'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg = ft_definetrial(cfg);</font></div>
<p style="margin:0px;font-stretch:normal;line-height:normal;min-height:12px">
<font face="Courier"> <br>
</font></p>
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)">
<font face="Courier"><span style="color:rgb(0,0,0)"> </span>
% preprocess</font></div>
<p style="margin:0px;font-stretch:normal;line-height:normal;min-height:12px">
<font face="Courier"> <br>
</font></p>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.demean =
<span style="color:rgb(160,32,240)">'yes'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.baselinewindow = [-0.175 0.025];<br>
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.lpfilter =
<span style="color:rgb(160,32,240)">'no'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.hpfilter =
<span style="color:rgb(160,32,240)">'no'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.dftfilter =
<span style="color:rgb(160,32,240)">'yes'</span>;</font></div>
</div>
<div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"><span style="white-space:pre-wrap"></span>split_files{1} = ft_preprocessing(cfg);
<span style="color:rgb(34,139,34)">%preprocess</span></font></div>
</div>
<div><span style="color:rgb(34,139,34)"><font face="Courier"><br>
</font></span></div>
<div><span style="color:rgb(34,139,34)"><font face="Courier"><br>
</font></span></div>
<div><span style="color:rgb(34,139,34)"><font face="Courier"><span style="white-space:pre-wrap"></span>%%%%%%%%%%%Downsampling%%%%%%%%%</font></span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier">
<span style="white-space:pre-wrap"></span>cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier">
<span style="white-space:pre-wrap"></span>cfg.resamplefs = 250;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier">
<span style="white-space:pre-wrap"></span>data = ft_resampledata(cfg, split_files{1});</font></div>
<div><font face="Courier"><br>
</font></div>
<div><font face="Courier"><br>
</font></div>
<div><font face="Courier"><span style="white-space:pre-wrap"></span>%%Visualisation</font></div>
<div><font face="Courier"><span style="white-space:pre-wrap"></span>cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.channel =
<span style="color:rgb(160,32,240)">'MEGGRAD'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> cfg.keeptrials =
<span style="color:rgb(160,32,240)">'yes'</span>; </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> data = ft_timelockanalysis(cfg,data);</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"><span style="white-space:pre-wrap"></span>Xlim([-0.2 0.6])</font></div>
<div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"> plot(data.time,squeeze(mean(data.trial(:,39,:),1))) </font></div>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"><br>
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier">As you can see from the plots attached, these signals are not identical when they should be (shouldn’t they?). The first plot is when I Use 2.5 seconds
post stim and the second is using 0.6. I’ve altered the xlim to show only up to 600ms on both. Also, can anyone explain these huge spikes at the beginning of trials, that’s my next problem to solve.</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier"><br>
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="Courier">Thanks</font></div>
<div><img id="gmail-m_-6457168803667585400A1BF5F22-8D25-4EC7-8437-0E1AFA994A0E" src="cid:177637d632ea17411e71"><img id="gmail-m_-6457168803667585400BEA436DE-DE1B-4212-84A1-748756FA28DF" src="cid:177637d632eb90abab52"></div>
</div>
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