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Hey Jan-Mathijs, Stephen,
<div class=""><br class="">
<div class="">Thanks for your help!</div>
<div class=""><br class="">
</div>
<div class="">Unfortunately that did not solve the issue. After some more digging, it looks like the problem is indeed caused by downsampling or demeaning. When I don’t use any downsampling, I have signal in different channels with different orders of magnitude
(see attached visual reject output). The channels with the huge black rectangles as signal are the very same that show this huge spike at the trial start after I downsample. However, when I don’t use any demeaning, the signals just look like flat lines. Please
see a subplot of 9 random GRAD channels too (created without demeaning).</div>
<div class=""><br class="">
</div>
<div class="">The issue must lie somewhere in this I imagine, although I am a bit clueless as to what it could be. Thanks for your time! <img apple-inline="yes" id="107085FF-1E5C-41DC-8ACE-16C2D98C1BF2" src="cid:3BAD4949-D703-4EEA-ADC4-B90B472753CD@home" class=""><img apple-inline="yes" id="86B66D56-A127-4BE2-961D-8B1942359178" src="cid:3F24B75A-14BF-4351-B878-FD9F8B220D3D@home" class=""><img apple-inline="yes" id="E6CBF7C3-FECC-4691-BD35-F39B1B8C8E95" src="cid:301EF19E-ADC2-468D-A645-E14E635D93BF@home" class=""></div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Benjy<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 4, 2021, at 10:47 AM, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Benjy,
<div class=""><br class="">
</div>
<div class="">You are probably looking at a downsampling artifact. I don’t understand why this happens, because the FT-code should be dealing with this ‘under the hood’.</div>
<div class=""><br class="">
</div>
<div class="">Could you - after the call to ft_redefinetrial - explicitly demean the epochs, prior to resampling, and see whether your problem disappears? i.e. you should do something like: cfg = [];</div>
<div class="">cfg.demean = ‘yes’; data = ft_preprocessing(cfg, data); (as mentioned on the data structure after re-epoching, but before resampling)</div>
<div class=""><br class="">
</div>
</div>
</div>
</blockquote>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class=""></div>
<div class="">I hope this helps.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 4 Feb 2021, at 10:57, Stephen Whitmarsh <<a href="mailto:stephen.whitmarsh@gmail.com" class="">stephen.whitmarsh@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Benjy,
<div class=""><br class="">
</div>
<div class="">Strange indeed. Does this still occur if you don't resample at all?</div>
<div class=""><br class="">
</div>
<div class="">If so, I don't know what else it could be. </div>
<div class=""><br class="">
</div>
<div class="">Unless someone else has an idea, perhaps you can create a small dataset and script with which we can reproduce the problem (on the latest FieldTrip version), then upload it to dropbox/google drive or similar,
</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Stephen</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Op do 4 feb. 2021 om 10:42 schreef Barnett, Benjy <<a href="mailto:benjy.barnett.20@ucl.ac.uk" class="">benjy.barnett.20@ucl.ac.uk</a>>:<br class="">
</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;" class="">Hey Stephen,
<div class=""><br class="">
</div>
<div class="">I believe I am plotting just single channels here, averaging over all the trials. After I call ft_timelockanalysis my dimord field is ‘rpt_chan_time’ and the dimensions of my trial field as 228 x 204 x 169, which makes sense as I am looking only
at the gradiometers, of which there are 204 in the neuromas set up.</div>
<div class=""><br class="">
</div>
<div class="">Then when I plot the signal I am using this command: </div>
<div class=""><span style="font-family:Courier" class=""><br class="">
</span></div>
<div class=""><span style="font-family:Courier" class="">plot(data_TL.time,squeeze(mean(data_TL.trial(:,39,:),1)))</span></div>
<div class="">
<div class=""><br class="">
</div>
Looking at, in this example, channel 39 on its own. As there are just 204 channels in the dimord field I don’t believe there are any reference channels added, and this jump occurs on ~20 different channels, and these vary across subjects. Like I say, I don’t
think the issue is with my data since the plot of all the data in one long trial looks quite normal. Indeed, when I call ft_rejectvisual, you get an idea of the scope of the problem as multiple different trials have these large spikes (image attached).</div>
<div class=""><br class="">
</div>
<div class="">All the best,</div>
<div class="">Benjy</div>
<div class=""><br class="">
</div>
<div class=""><span id="cid:1776c74c960a989de7d1" class=""><sub02.png></span><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 3, 2021, at 6:05 PM, Stephen Whitmarsh <<a href="mailto:stephen.whitmarsh@gmail.com" target="_blank" class="">stephen.whitmarsh@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Hi Benjy,
<div class=""><br class="">
</div>
<div class="">Just a though - but am I right that you are plotting an average over channels? Can you look at the channels individually and see on which channels the jumps occur? Might you accidentally be adding a reference/external/trigger channel to the average?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Stephen</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Op wo 3 feb. 2021 om 18:42 schreef Barnett, Benjy <<a href="mailto:benjy.barnett.20@ucl.ac.uk" target="_blank" class="">benjy.barnett.20@ucl.ac.uk</a>>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><span style="font-size:14px" class="">Hey Stephen,</span>
<div class=""><span style="font-size:14px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:14px" class="">Thanks for your help! Whilst this certainly answers my question about the slight difference between different trial lengths, the huge spikes at the beginning of trials remains regardless of whether I filter
the data as a whole first, or if I segment into trials and then filter. Here’s my code for doing the filtering first (my code for the alternative way is in my initial post):</span></div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg = [];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg.dataset = full_path;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg.continuous =
<span style="color:rgb(160,32,240)" class="">'yes'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)" class="">
<span class=""> </span>%cfg.demean = 'yes';</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)" class="">
%cfg.baselinewindow = baselinewindow;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg.lpfilter =
<span style="color:rgb(160,32,240)" class="">'no'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg.hpfilter =
<span style="color:rgb(160,32,240)" class="">'no'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">cfg.dftfilter =
<span style="color:rgb(160,32,240)" class="">'yes'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:12px" class="">
<br class="">
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">data = ft_preprocessing(cfg);</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg=[];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.dataset=full_path;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.trialdef.prestim=0.175;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.trialdef.poststim=0.600;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.trialdef.eventvalue=[6 7];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.trialdef.eventtype=<span style="color:rgb(160,32,240)" class="">'STI101'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg = ft_definetrial(cfg);</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
trl = cfg.trl(:,1:3);</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:13px" class="">
<br class="">
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg = [];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.trl = trl;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
data_segmented = ft_redefinetrial(cfg,data);</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:13px" class="">
<br class="">
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg = [];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.resamplefs = 250;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
data_ds = ft_resampledata(cfg, data_segmented);</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg = [];</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.channel = <span style="color:rgb(160,32,240)" class="">'MEGGRAD'</span>;</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
cfg.keeptrials = <span style="color:rgb(160,32,240)" class="">'yes'</span>; </div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
data_TL = ft_timelockanalysis(cfg,data_ds);</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier" class="">
plot(data_TL.time,squeeze(mean(data_TL.trial(:,39,:),1))) <span style="color:rgb(34,139,34)" class="">
%17, 23 and 39 are examples of spikes in channels</span></div>
</div>
<div class=""><span id="gmail-m_5459719455365994611cid:177690f1a975b206ef61" class=""><PastedGraphic-1.png></span><span id="gmail-m_5459719455365994611cid:177690f1a975b2e86772" class=""><PastedGraphic-2.png></span></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><span style="font-size:14px" class="">I’m still seeing spikes as in the images attached. Something else strange: when I change the poststim parameter to 0.075 instead of 0.175 (keeping everything else equal), the direction of the spike completely
switches (see third image attached). This happens regardless or ft_definetrial/preprocessing order. Moreover, when I look at the signal across the single trial encapsulating all the data (i.e. before segmentation), there are none of these huge spikes where
every event would be, only a few spikes that I assume are SQUID jumps.</span></div>
<div class=""><span id="gmail-m_5459719455365994611cid:177690f1a977e5fd32b3" class=""><Screenshot 2021-02-03 at 11.29.20 AM.png></span><span id="gmail-m_5459719455365994611cid:177690f1a974341a9734" class=""><long_trial_single_channel.png></span></div>
<div class=""><span style="font-size:14px" class="">This makes me think the issue is coming at the ft_definetrial() step. But since this does not read in the actual MEG data, I can’t work out what is causing this effect, it certainly doesn’t seem to be an issue
with my data. I’ve added a couple of lines to the ft_trialfun_general function, so to be sure I’ve removed them and am just using the default version yet the problem is persisting. </span></div>
<div class=""><span style="font-size:14px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:14px" class="">Any assistance is of course greatly appreciated. Thanks!</span></div>
<div class=""><span style="font-size:14px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:14px" class="">Benjy</span><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 2, 2021, at 4:14 PM, Stephen Whitmarsh <<a href="mailto:stephen.whitmarsh@gmail.com" target="_blank" class="">stephen.whitmarsh@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Hey Benjy,
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">To avoid this, and to create a fair comparison between your different trial duration segmentation, I would do the following:</div>
<div class=""><br class="">
</div>
<div class="">- 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 class="">- segment your filtered data into trials using ft_redefinetrial.</div>
<div class="">
<div class="">- do your resampling </div>
<div class=""></div>
</div>
<div class="">- check the different triallengths.</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Have fun,<br class="">
</div>
<div class="">Stephen</div>
</div>
<br class="">
<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" target="_blank" class="">benjy.barnett.20@ucl.ac.uk</a>>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><font face="Courier" class="">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 class=""><font face="Courier" class=""><br class="">
</font></div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)" class="">
<font face="Courier" class=""><span class=""><span style="white-space:pre-wrap" class=""></span> </span>% define trials</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.dataset = full_path;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.trialdef.prestim = 0.175; </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.trialdef.poststim = 0.6;
<span style="color:rgb(34,139,34)" class="">% compare with 2.5 seconds</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.trialdef.eventvalue = [6 7 9];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.trialdef.eventtype =
<span style="color:rgb(160,32,240)" class="">'STI101'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg = ft_definetrial(cfg);</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:12px" class="">
<font face="Courier" class=""> <br class="">
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal;color:rgb(34,139,34)" class="">
<font face="Courier" class=""><span class=""> </span>% preprocess</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:12px" class="">
<font face="Courier" class=""> <br class="">
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.demean =
<span style="color:rgb(160,32,240)" class="">'yes'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.baselinewindow = [-0.175 0.025];<br class="">
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.lpfilter =
<span style="color:rgb(160,32,240)" class="">'no'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.hpfilter =
<span style="color:rgb(160,32,240)" class="">'no'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.dftfilter =
<span style="color:rgb(160,32,240)" class="">'yes'</span>;</font></div>
</div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""><span style="white-space:pre-wrap" class=""></span>split_files{1} = ft_preprocessing(cfg);
<span style="color:rgb(34,139,34)" class="">%preprocess</span></font></div>
</div>
<div class=""><span style="color:rgb(34,139,34)" class=""><font face="Courier" class=""><br class="">
</font></span></div>
<div class=""><span style="color:rgb(34,139,34)" class=""><font face="Courier" class=""><br class="">
</font></span></div>
<div class=""><span style="color:rgb(34,139,34)" class=""><font face="Courier" class=""><span style="white-space:pre-wrap" class=""></span>%%%%%%%%%%%Downsampling%%%%%%%%%</font></span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class="">
<span style="white-space:pre-wrap" class=""></span>cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class="">
<span style="white-space:pre-wrap" class=""></span>cfg.resamplefs = 250;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class="">
<span style="white-space:pre-wrap" class=""></span>data = ft_resampledata(cfg, split_files{1});</font></div>
<div class=""><font face="Courier" class=""><br class="">
</font></div>
<div class=""><font face="Courier" class=""><br class="">
</font></div>
<div class=""><font face="Courier" class=""><span style="white-space:pre-wrap" class=""></span>%%Visualisation</font></div>
<div class=""><font face="Courier" class=""><span style="white-space:pre-wrap" class=""></span>cfg = [];</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.channel =
<span style="color:rgb(160,32,240)" class="">'MEGGRAD'</span>;</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> cfg.keeptrials =
<span style="color:rgb(160,32,240)" class="">'yes'</span>; </font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> data = ft_timelockanalysis(cfg,data);</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""><span style="white-space:pre-wrap" class=""></span>Xlim([-0.2 0.6])</font></div>
<div class="">
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""> plot(data.time,squeeze(mean(data.trial(:,39,:),1))) </font></div>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class=""><br class="">
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class="">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" class=""><font face="Courier" class=""><br class="">
</font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Courier" class="">Thanks</font></div>
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