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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">Dear Sophie,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">You have correctly identified that the error arises from the filter
padding process. From my experience, if there are gaps (i.e., no available data points) between your trials, this will lead to NaN values during filter padding. While I am not fully aware of your data preprocessing and trial selection methods that leads to
the <i>data_segment</i>, it believe that your trials have gaps in between. For instance, inspecting
<i>data_segment.samplenfo</i> might reveal that the trials do not consist of continuous, uncut segments.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">One option is to
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Calibri",sans-serif;color:black;mso-ligatures:none;mso-fareast-language:NL">set the filter padding to 0</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">,
</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">but this won’t take care of the filter-induced edge effects</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">.
</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">Another option is to go back in your analysis and change the way you segment your data. When you split your data into trials do not leave any gaps between trials. For example, split your
signal in 30 seconds trials without gaps in between.</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Calibri",sans-serif;color:#212121;mso-ligatures:none;mso-fareast-language:NL"> O</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">r
if you leave gaps between trials, make sure to keep 0.1 sec more in the beginning and the end of each trial for
</span><i><span lang="EN-US" style="font-size:12.0pt;font-family:"Calibri",sans-serif;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.fltpadding = 0.1</span></i><span lang="EN-US" style="font-size:12.0pt;font-family:"Calibri",sans-serif;color:black;mso-ligatures:none;mso-fareast-language:NL">
to work properly</span><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">.
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Calibri",sans-serif;color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">Best regards,<br>
Konstantinos Tsilimparis<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;mso-ligatures:none;mso-fareast-language:EN-GB"> fieldtrip
<fieldtrip-bounces@science.ru.nl> <b>On Behalf Of </b>Schubert, E.S. (Sophie) via fieldtrip<br>
<b>Sent:</b> Wednesday, July 3, 2024 4:14 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> Schubert, E.S. (Sophie) <E.S.Schubert@umcutrecht.nl><br>
<b>Subject:</b> [FieldTrip] Issue with NaN values using ft_artifact_zvalue<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Dear FieldTrip Support Team,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">I am writing to seek assistance with an issue I am encountering while using the ft_artifact_zvalue function in FieldTrip for artifact rejection.
Despite my data containing no NaN values initially, I receive an error during the bandpass filtering process indicating that the input is expected to be finite.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Here is a detailed description of the problem:</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">searching for artifacts in 2 channels</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Warning: data contains NaNs, not all processing methods are robust to NaNs, so the NaNs</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">might spread </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Warning: data contains NaN values </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error using filtfilt>efiltfilt</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error using filtfilt</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Expected input to be finite.</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error in filtfilt (line 102)</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> y = efiltfilt(b,a,x);</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error in filter_with_correction (line 73)</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> filt = filtfilt(B, A, dat')';</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error in ft_preproc_bandpassfilter (line 300)</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> filt = filter_with_correction(B,A,dat,dir,usefftfilt);</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error in preproc (line 405)</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">if strcmp(cfg.bpfilter, 'yes'), dat = ft_preproc_bandpassfilter(dat, fsample, cfg.bpfreq, cfg.bpfiltord, cfg.bpfilttype, cfg.bpfiltdir,
cfg.bpinstabilityfix, cfg.bpfiltdf, cfg.bpfiltwintype, cfg.bpfiltdev, cfg.plotfiltresp, cfg.usefftfilt); end</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> </span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Error in ft_artifact_zvalue (line 315)</span></i><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"> thisdat = preproc(thisdat, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(thisdat,2)), cfg.artfctdef.zvalue, fltpadding,
fltpadding);<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></i></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">The code that I use:</span></b><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">frontalEye = {'EOG LOC-A2', 'EOG ROC-A2'}; % for artifact rejection</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg = [];</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.channel = frontalEye;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.cutoff = 2.5;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.trlpadding = 0;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.artpadding = 0.4;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.fltpadding = 0.1;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.bpfilter = 'yes';</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.bpfreq = [0.5 2];</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.bpfiltord = 4;</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.bpfilttype = 'but';</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.hilbert = 'yes';</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">cfg.artfctdef.zvalue.interactive = 'no';</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">[cfg, artifact_EOG_eye] = ft_artifact_zvalue(cfg, data_segmented);</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="NL" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span lang="NL" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Important notes:</span></b><span lang="NL" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoNormal" style="color:black;mso-list:l1 level1 lfo3"><span lang="EN-US" style="font-size:12.0pt;mso-ligatures:none;mso-fareast-language:NL">I have checked and verified that the data does not contain any NaN values before the filtering process.</span><span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-list:l1 level1 lfo3"><span lang="EN-US" style="font-size:12.0pt;mso-ligatures:none;mso-fareast-language:NL">I have tried different configurations, including setting the padding to 0, which prevents the error</span><span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">It appears that NaN values are being introduced during the filtering process, but I am unable to determine the cause. I understand that the
filterpadding specifies how much extra data around each trial's segment is read from the file. This extra data (padding) is used to mitigate edge artifacts that can occur after applying filters to the data. However, given the encountered error, I am uncertain
if I am utilizing this function correctly. Could you please provide guidance on how to resolve this issue? </span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Thank you for your support!</span><span lang="EN-US" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:NL">Sophie Schubert</span><span lang="NL" style="color:#212121;mso-ligatures:none;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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