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<p class="MsoNormal">Hey Georgios-<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This can definitely be a tricky problem. I have run into this in the past when trying to sort responses to TMS based on when the stimulus occurs relative to the phase. My colleagues and I came up with a non-fieldtrip implementation of this
which is published here: <a href="https://academic.oup.com/cercor/article/29/9/3766/5218042">
https://academic.oup.com/cercor/article/29/9/3766/5218042</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">What happens is because filters use a window of samples, anything after the stimulus can contaminate phase estimates at the stimulus timepoint. We ended up using a clamping approach in which all values beginning 1 sample before stimulus
to the end of the epoch are clamped to the value of the sample preceding the stimulus. Then we use a one pass FIR filter and correct for the phase delay to get the filtered data.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve attached a function I wrote to perform this process– you would have to modify some of the parameters in the function (sampling rate, filtering freqs, etc). If you end up using this please cite the above paper in which we’ve validated
the phase estimates this filtering approach produces. After you get the filtered data, you can do the Hilbert and phase extraction as you mention.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hope this helps-<o:p></o:p></p>
<p class="MsoNormal">Sara<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">george michael <gmichael_@hotmail.com><br>
<b>Reply-To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Thursday, June 18, 2020 at 9:11 AM<br>
<b>To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject: </b>[FieldTrip] single-trial phase at stimulus onset using Hilbert transform<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Dear Fieldtrip Community,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">I am trying to extract the alpha phase at stimulus onset from single trials.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">My approach is to :<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">1) Band-pass filter the trial segments from -500ms to 0 (±1Hz around individual alpha frequency).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">I use the filter 'firws' and filter direction 'onepass' to avoid smearing poststimulus activity into the prestimulus interval.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">2) Compute Hilbert transform to extract the instantaneous phase of the bandpass signal.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">3) Select the phase at the last sample (t=0) as the one representing phase at stimulus onset.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> cfg=[];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.channel = 'O1';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.bpfilter='yes';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.bpfreq=[foi-1 foi+1];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.bpfilttype= 'firws';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.bpfiltdir= 'onepass';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">cfg.hilbert='angle';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">phase = ft_preprocessing(cfg , trials_prestim);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> for tr=1:length(phase .trial)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> phase_onset(tr,:)=phase .trial{tr}(:,end); % select phase at last sample<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> end<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">The problem is that the band-bass signal looks quite weird at the right edge, towards t=0s (see attached figure). <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Do you have any idea what would be the reason for this problem?
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">And which would be the optimal way to extract phase at stimulus onset?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal">Many thanks,<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Georgios<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">-----------------------<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Georgios Michail, MSc.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Department of Psychiatry and Psychotherapy<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Charite-Universitätsmedizin Berlin<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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