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That would be awesome, Dr. Ivaylo!</div>
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I've been trying to implement it for weeks!</div>
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Thank you so much for any help</div>
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Eleonora </div>
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<span style="margin: 0px; font-size: 16px; font-family: Calibri, Arial, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; text-align: start; background-color: white;"><font size="2" face="Calibri,Arial,Helvetica,sans-serif" style="color: rgb(117, 123, 128);"><span style="margin:0px"><b><font size="2" style="color: rgb(117, 123, 128);"><span style="margin:0px; font-size:11pt"><span style="margin: 0px; font-size: 13.31px; font-family: Calibri, sans-serif; color: rgb(222, 106, 25);">Eleonora
Parrotta, Doctoral Researcher in Social Neuroscience </span></span></font></b></span></font></span>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Da:</b> Ivaylo Iotchev <ivaylo.iotchev@gmail.com><br>
<b>Inviato:</b> giovedì 25 maggio 2023 14:50<br>
<b>A:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> eleonora parrotta <eleonora_p@hotmail.it><br>
<b>Oggetto:</b> Re: [FieldTrip] automatic artifact rejection based on voltage threshold</font>
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<div dir="ltr">Hey Eleonora,<br>
<br>
I might be able to send you some lines tomorrow which implement thresholding, these lines do not make direct use of FieldTrip I think, but they are MATLAB intern and thus can be coordinated within a script that uses Fieldtrip functions, too (basically that's
what we are doing at the moment).<br>
<br>
Best wishes,<br>
<br>
(Dr.) Ivaylo (Ivo) Iotchev</div>
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<div dir="ltr" class="x_gmail_attr">Am Do., 25. Mai 2023 um 15:45 Uhr schrieb eleonora parrotta via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>>:<br>
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<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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Dear Fieldtrippers,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
I am trying to implement an automatic artifact rejection on epoched data. </div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
The aim of this process would be to compare the same dataset, analyzed both in fieldtrip and eeglab. To do so, I would need to efficiently implement the same EEGLAB parameters used for the artifact rejection in fieldtrip. </div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
I have two options</div>
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<div><span>
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<div>
<ol>
<li><span><span style="margin:0px">eliminate the trials based on a</span></span> peak-to-peak artifact rejection, which detects and remove trials in which the EEG signal exceeds of a threshold of 100 microvolt</li></ol>
<ol start="2">
<li><span>eliminate the trials based on simple threshold voltage, that is, eliminate trials in which the voltage exceeds of +- 50 microvolts.</span><br>
</li></ol>
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</span></div>
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
Both options would be fine as both are implemented in eeglab, but I do not manage to implement neither of the two into fieldtrip.</div>
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I've tried to use both ft_artifact_threshold and ft_rejectartifact, even by combining the two.</div>
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ft_rejectartifact is not able not detect artifacts in the data, the output is always :</div>
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%artifact rejection
<div>cfg = [];</div>
<div>cfg.artfctdef.channel = [1:28 31:65];</div>
<div>cfg.artfctdef.threshold.min = -50;</div>
<div>cfg.artfctdef.threshold.max = 50;</div>
<div>cfg.artfctdef.prestim = -0.1;</div>
<div>cfg.artfctdef.poststim = 0.6;</div>
<div>cfg.artfctdef.window = 'trial';</div>
data_clean = ft_rejectartifact(cfg, clean_data);<br>
</div>
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<br>
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
the call to "ft_preprocessing" took 111 seconds
<div>rejected 0 trials completely</div>
<div>rejected 0 trials partially</div>
<div>filled parts of 0 trials with NaNs</div>
<div>filled parts of 0 trials with zeros</div>
filled parts of 0 trials with a specified value <br>
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<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">This is an example of what I get when using the functions together..</span></div>
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<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)"><br>
</span></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
<span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">cfg = [];</span><br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
<div>cfg.continuous = 'no';</div>
<div>cfg.artfctdef.channel = {'all', '-ECG1', '-ECG2', '-IO'};</div>
<div>cfg.dataset =clean_data.trial(:,:);</div>
<div>% cfg.artfctdef.threshold.min = -50;</div>
<div>% cfg.artfctdef.threshold.max = 50;</div>
<div>% cfg.artfctdef.threshold.range=100;</div>
<div>cfg.artfctdef.prestim = -0.1;</div>
<div>cfg.artfctdef.poststim = 0.6;</div>
<div>cfg.trl=trl;</div>
<div>[~, artData] = ft_artifact_threshold(cfg, clean_data);</div>
<div><br>
</div>
<div>cfg = [];</div>
<div>cfg.artfctdef.xxx.artifact = artData;</div>
<div>cfg.artfctdef.reject = 'complete';</div>
<div>fnData = ft_rejectartifact(cfg, clean_data);</div>
</div>
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
The output seems to not be able to read the trials information, as it does not mark the trials but only segments in which there are artifacts: </div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
searching for artifacts in 65 channels
<div>applying preprocessing options</div>
<div>searching in trial 643 from 643</div>
<div>detected 7172 artifacts</div>
the call to "ft_artifact_threshold" took 25 seconds</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
>>
<div>cfg = [];</div>
<div>cfg.artfctdef.xxx.artifact = artData;</div>
<div>cfg.artfctdef.reject = 'complete';</div>
<div>fnData = ft_rejectartifact(cfg, clean_data);</div>
<div>detected 1 xxx artifacts</div>
<div>Index in position 2 exceeds array bounds. Index must not exceed 1.</div>
<div><br>
</div>
<div>Error in ft_rejectartifact (line 305)</div>
endsample = artifact{i}(:,2);<br>
</div>
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Please help me!!</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(0,0,0)">
Any support is appreciated <br>
Thank you very much </div>
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<span style="margin:0px; font-size:16px; font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; text-align:start; background-color:white"><font size="2" face="Calibri,Arial,Helvetica,sans-serif" style="color:rgb(117,123,128)"><span style="margin:0px"><b><font size="2" style="color:rgb(117,123,128)"><span style="margin:0px; font-size:11pt"><span style="margin:0px; font-size:13.31px; font-family:Calibri,sans-serif; color:rgb(222,106,25)">Eleonora
Parrotta, Doctoral Researcher in Social Neuroscience </span></span></font></b></span></font></span>
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University of Aberdeen | Aberdeen |<span> </span><span style="margin:0px; font-size:13.32px; font-family:Arial,sans-serif,serif,EmojiFont; color:rgb(51,51,51); background-color:white">AB24 3FX</span></span></div>
<span style="margin:0px"><span style="margin:0px; color:rgb(117,123,128)"><span style="margin:0px; font-size:13.32px; font-family:Arial,sans-serif,serif,EmojiFont; color:rgb(51,51,51); background-color:white"><span style="margin:0px; font-family:Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont; background-color:white"><span style="margin:0px"><a href="mailto:e.parrotta.20@abdn.ac.uk" target="_blank">e.parrotta.20@abdn.ac.uk</a></span></span></span></span></span></span></span></font></span></font></div>
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