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<p class="MsoNormal">Dear FieldTrip community,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My name is Hans Revers. I am a PhD student in the Cognitive Neuropsychology department at Tilburg University, working on decoding emotions from EEG patterns.
<o:p></o:p></p>
<p class="MsoNormal">I would appreciate your insight on how to handle NaNs in TFR power spectra resulting from partial artifact rejection.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We have trials of 90 seconds duration, with artifacts marked from pre-processing in Brain Vision Analyzer. We wish to do a time-frequency analysis (montecarlo cluster analysis) and a classification (mvpa-light). We would want to exclude
only the artefact parts per trial while retaining the non-artifact parts and the temporal information. Partial rejection of artifacts appears to be the way to achieve this (<a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2018-May/012138.html">https://mailman.science.ru.nl/pipermail/fieldtrip/2018-May/012138.html</a>).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> % reject artefact cfg<o:p></o:p></p>
<p class="MsoNormal"> cfg_artifact = [];<o:p></o:p></p>
<p class="MsoNormal"> cfg_artifact.artfctdef.reject = 'partial'; <o:p></o:p></p>
<p class="MsoNormal"> % remove artifacts<o:p></o:p></p>
<p class="MsoNormal"> cfg_artifact.artfctdef.xxx.artifact = formatArtifactList(Dairy_per_pp(pp_i).cfg);
<o:p></o:p></p>
<p class="MsoNormal"> % The formatArtifactList() function returns an Nx2 matrix containing
<o:p></o:p></p>
<p class="MsoNormal"> % the start/end samples of each ‘Bad Interval’.<o:p></o:p></p>
<p class="MsoNormal"> ConditionA_per_pp(pp_i) = ft_rejectartifact(cfg_artifact, ConditionA _per_pp(pp_i));<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This works as expected. Artifact intervals are stored in the cfg of the data in artfcdef.xxx.artifact. Next, ft_freqanalysis results in NaNs in the power spectrum for these intervals with a half taper width before and after. Baseline normalization
with ft_freqbaseline seems to handle these NaNs just fine. So far, so good. (I guess we need to make sure that the baseline does not consist of solely NaNs.)<o:p></o:p></p>
<p class="MsoNormal">However, when we average over participants with ft_freqgrandaverage, the GA results in a NaN for each time bin that has a NaN for one (or more) of the participants. We had expected a nanmean result.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This could be easily fixed by calculating our own nanmean GA powerspectrum, but I am hesitant to alter the intended workings of FieldTrip and I have the following concerns:
<o:p></o:p></p>
<p class="MsoNormal">Question 1) Are there reasons not to use a nanmean GA? <o:p>
</o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ft_freqstatistics appears to run unaffected by the presence of NaNs in the per-pp power spectra. We are using non-parametric montecarlo cluster analysis with depsamplesT test. ft_statfun_depsamplesT seems to use a nanmean in the calculation
of the statistics. <o:p></o:p></p>
<p class="MsoNormal">Question 2) Can we assume that the statistics are reliable? Or do the NaNs compromise the statistics?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And similarly <o:p></o:p></p>
<p class="MsoNormal">Question 3) Will mvpa classification results be reliable?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help would be appreciated.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kind regards,<span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:X-NONE"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:X-NONE">Hans Revers<o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://www.tilburguniversity.edu/about/schools/socialsciences/organization/departments/cognitive-neuropsychology.htm"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:X-NONE">Department of Cognitive
Neuropsychology</span></a><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:X-NONE"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;mso-fareast-language:X-NONE">Tilburg University<o:p></o:p></span></p>
<p class="MsoNormal"><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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