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Hi Sara,</div>
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thank you very much for the suggestion and for sharing the script.</div>
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I 'll definitely give it a try and compare it with the outcome from Fieldtrip (using firws and onepass-zerophase filter).</div>
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All the best,</div>
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Georgios<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Hussain, Sara (NIH/NINDS) [F] <sara.hussain@nih.gov><br>
<b>Sent:</b> Thursday, June 18, 2020 16:03<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] single-trial phase at stimulus onset using Hilbert transform</font>
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<span style="color:black">I sent this reply to your question Georgios but it has yet to go through. Trying again – see below.
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<span style="color:black">Hey Georgios-</span></p>
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<span style="color:black">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://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Facademic.oup.com%2Fcercor%2Farticle%2F29%2F9%2F3766%2F5218042&data=02%7C01%7C%7C56db724561a84059bb3f08d8139079b0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637280858538599729&sdata=GkObc1Qr3AlUeQ9RY9zLWHX2DjXIpR9vaLsGlWzZZ%2F8%3D&reserved=0" originalsrc="https://academic.oup.com/cercor/article/29/9/3766/5218042" shash="tEndYc8Tar2y9fR40hOzYfg7FX1Z8sf1oJTtxTbSwBW0m7/tuA9/R5h/N3Q0d/P056myZr1SL7IleBEfk0x6dG7W8N3shnZB4q/FlDOxfldpJObOEE8nEGIomGPTlBtkGL0kpYPWxFpPqNJvoD7gCzMV7cexY1snGab+YlYuJfk=" title="https://academic.oup.com/cercor/article/29/9/3766/5218042"><span style="color:#044A91">https://academic.oup.com/cercor/article/29/9/3766/5218042</span></a></span></p>
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<span style="color:black">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. </span></p>
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<span style="color:black">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.</span></p>
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<span style="color:black">Hope this helps-</span></p>
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<span style="color:black">Sara</span></p>
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<b><span style="font-size:12.0pt; color:black">From: </span></b><span style="font-size:12.0pt; color:black">Tzvetan Popov <tzvetan.popov@uni-konstanz.de><br>
<b>Reply-To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Thursday, June 18, 2020 at 9:56 AM<br>
<b>To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject: </b>Re: [FieldTrip] single-trial phase at stimulus onset using Hilbert transform</span></p>
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Using filters is always a “problem”. A symmetric filter will at least not misplace your signal of interest. My reply referred to the “weirdness at the right edge”. </p>
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Best</p>
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tzvetan</p>
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Am 18.06.2020 um 14:44 schrieb george michael <<a href="mailto:gmichael_@hotmail.com">gmichael_@hotmail.com</a>>:</p>
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<span style="font-size:12.0pt">Dear Tzvetan,</span></p>
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<span style="font-size:12.0pt">thanks you for the quick reply.</span></p>
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<span style="font-size:12.0pt">Wouldn't be a problem to use "onepass-zerophase" or "twopass" given that I am interested in phase at stimulus onset?</span></p>
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<span style="font-size:12.0pt">Don't both filter-types smear poststimulus activity into the prestimulus interval?</span></p>
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<span style="font-size:12.0pt">Best,</span></p>
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<span style="font-size:12.0pt">Georgios</span></p>
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<b>From:</b><span class="x_apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>> on behalf of Tzvetan Popov <<a href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a>><br>
<b>Sent:</b><span class="x_apple-converted-space"> </span>Thursday, June 18, 2020 14:27<br>
<b>To:</b><span class="x_apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
<b>Subject:</b><span class="x_apple-converted-space"> </span>Re: [FieldTrip] single-trial phase at stimulus onset using Hilbert transform<span style="font-size:9.0pt; font-family:Helvetica"></span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">Dear Georgios,</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">the reason is your cfg.bpfiltdir = ‘onepass’. This should be zero phase or twopass filter. Yet, you will still get filter artefacts at the edges. I suggest you should re-segment your data, e.g. -1000 to 500ms,
filter and then re-segment to -500 to 0 again.</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">Good luck,</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">tzvetan</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">Am 18.06.2020 um 14:14 schrieb george michael <<a href="mailto:gmichael_@hotmail.com">gmichael_@hotmail.com</a>>:</span></p>
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<span style="font-size:12.0pt">Dear Fieldtrip Community,</span></p>
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<span style="font-size:12.0pt">I am trying to extract the alpha phase at stimulus onset from single trials.<span class="x_xapple-converted-space"> </span></span></p>
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<span style="font-size:12.0pt">My approach is to :</span></p>
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<span style="font-size:12.0pt">1) Band-pass filter the trial segments from -500ms to 0 (±1Hz around individual alpha frequency).</span></p>
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<span style="font-size:12.0pt">I use the filter 'firws' and filter direction 'onepass' to avoid smearing poststimulus activity into the prestimulus interval.</span></p>
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<span style="font-size:12.0pt">2) Compute Hilbert transform to extract the instantaneous phase of the bandpass signal.<span class="x_xapple-converted-space"> </span></span></p>
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<span style="font-size:12.0pt">3) Select the phase at the last sample (t=0) as the one representing phase at stimulus onset.</span></p>
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<span style="font-size:12.0pt"> cfg=[];</span></p>
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<span style="font-size:12.0pt">cfg.channel = 'O1';</span></p>
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<span style="font-size:12.0pt">cfg.bpfilter='yes';</span></p>
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<span style="font-size:12.0pt">cfg.bpfreq=[foi-1 foi+1];</span></p>
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<span style="font-size:12.0pt">cfg.bpfilttype= 'firws';</span></p>
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<span style="font-size:12.0pt">cfg.bpfiltdir= 'onepass';</span></p>
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<span style="font-size:12.0pt">cfg.hilbert='angle';</span></p>
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<span style="font-size:12.0pt">phase = ft_preprocessing(cfg , trials_prestim);</span></p>
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<span style="font-size:12.0pt"> for tr=1:length(phase .trial)</span></p>
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<span style="font-size:12.0pt"> phase_onset(tr,:)=phase<span class="x_xapple-converted-space"> </span>.trial{tr}(:,end); % select phase at last sample</span></p>
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<span style="font-size:12.0pt"> end</span></p>
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<span style="font-size:12.0pt">The problem is that the band-bass signal looks quite weird at the right edge, towards t=0s (see attached figure). </span></p>
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<span style="font-size:12.0pt">Do you have any idea what would be the reason for this problem?<span class="x_xapple-converted-space"> </span></span></p>
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<span style="font-size:12.0pt">And which would be the optimal way to extract phase at stimulus onset?</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica">Many thanks,</span></p>
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<span style="font-size:12.0pt">Georgios</span></p>
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<span style="font-size:12.0pt">-----------------------</span></p>
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<span style="font-size:12.0pt">Georgios Michail, MSc.</span></p>
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<span style="font-size:12.0pt">Department of Psychiatry and Psychotherapy</span></p>
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<span style="font-size:12.0pt">Charite-Universitätsmedizin Berlin</span></p>
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<span style="font-size:9.0pt; font-family:Helvetica"><bandpass_alpha_singlesubj.png>_______________________________________________<br>
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<a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7C%7C56db724561a84059bb3f08d8139079b0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637280858538629711&sdata=2xfm7gr%2BmKlkmWJCak2FNS8WFgfs2GYgjr5phJp22Ck%3D&reserved=0" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="TuoZTta7A+iD8qqbGrFI08tV7iQHazQYKjlvO1bMrpY7iK+GQ5KEiN4mRhGTnXIUXDCq965fR9cP2mPhdBy0Dikj0UpAw9hIN+DWQ5c5tDZIo68GWD1gEZ/2ejWtOxwWt5+8bsLUhn6Lc0+wk2lGuzNxhMrtlDOKYGeW0DuUwug=">https://doi.org/10.1371/journal.pcbi.1002202</a></span></p>
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</span><a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7C%7C56db724561a84059bb3f08d8139079b0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637280858538659694&sdata=jVLuHCF0ey%2FF3FL6OJA25vC7pyRkXMPcX9JkDa7pBus%3D&reserved=0" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="u/vVMCMppgCp+7iXaI0NG3csUNL6RNXSDqbkOdnaPFxBuUjvPQlTp/vInwUnDFf3BAYQp0XpLoWgC0UdxaVOkUMQMIg9AfuHXcd2StaurNoRxloZOfHv48i+HzHYjGun7uWJFlrSOJgP0J9CCdaOZ6qxqr1Z77NLYsfrQ04xHYk="><span style="font-size:9.0pt; font-family:Helvetica">https://doi.org/10.1371/journal.pcbi.1002202</span></a></p>
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