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Dear Maria,
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<div class="">Thanks for your clear message and diagnostics so far. Just for the clear picture: the error is thrown by ft_artifact_threshold, isn’t it? If I read through the code of this function, I get the impression that you might get yourself back into the
game, if you specify cfg.continuous = ‘yes’ for the cfg into ft_artifact_threshold. Although, this feels a bit at odds with the representation of the data that you give as an input to the function, because the time-axes of the individual trials clearly is
not continuous. However, the sampelinfo field of the data object is still consistent with a continuous data representation (on disk). It’s the sampleinfo field that ft_fetch_data uses under the hood to determine the overlapping samples. I think that the error
will convert into a warning with cfg.continuous = ‘yes’; (unless you have already tried this and can disconfirm my hunch). So, long story short, I’d recommend cfg.continuous = ‘yes’.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 26 Oct 2023, at 11:31, Hartog, M.M.J. den (Maria) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Dear community,</div>
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My name is Maria den Hartog and I am a PhD candidate at the Centre for Language Studies (CLS) at Radboud University in Nijmegen. I am currently preprocessing data from an ERP reading experiment about the processing of pronouns of address (e.g. he, she, they)
within a text. </div>
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I want to use automatic artifact rejection to remove full trials with signal exceeding +-100 µV as part of my preprocessing pipeline, but I get an error message indicating that 'some of the requested samples occur twice in the data and have conflicting values'.
This is true, and it is a consequence of the naturalistic reading paradigm I used. My trials run from -200 ms prestimulus to 1000 ms poststimulus. The t = 0 of each trial is the onset of a pronoun within a text, and the pronouns can occur less than 1000 ms
after each other (e.g., the stimuli are<span class="Apple-converted-space"> </span><b class="">he<span class="Apple-converted-space"> </span></b>and<span class="Apple-converted-space"> </span><b class="">his<span class="Apple-converted-space"> </span></b>in
'<b class="">He</b><span class="Apple-converted-space"> </span>looked at<span class="Apple-converted-space"> </span><b class="">his<span class="Apple-converted-space"> </span></b>cat.'). I have baselined my trials to the 200 ms window up to the stimulus, meaning
the same sample can have different values in different trials.</div>
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The code I use for artifact rejection is:</div>
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<div class="rtcContent" style="padding: 30px;"><span class="lineNode" style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-weight: normal;"><span class=""><span class="ContentPasted2"> cfg = [];</span></span></span>
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<span class=""><span class="ContentPasted2"> cfg.continuous =<span class="Apple-converted-space"> </span></span><span class="ContentPasted2" style="color: rgb(167, 9, 245);">'no'</span><span class="ContentPasted2">;</span></span></div>
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<span class=""><span class="ContentPasted2"> cfg.artfctdef.threshold.min = -100;</span></span></div>
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<span class=""><span class="ContentPasted2"> cfg.artfctdef.threshold.max = 100;</span></span></div>
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<span class=""><span class="ContentPasted2"> art = ft_artifact_threshold(cfg,data);</span></span></div>
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<span class=""><span class="ContentPasted2"> cfg = [];</span></span></div>
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<span class=""><span class="ContentPasted2"> cfg.artfctdef.xxx.artifact = art.artfctdef.threshold.artifact;</span></span></div>
<span class="lineNode" style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-weight: normal;"><span class=""><span class="ContentPasted2"> data_forERP = ft_rejectartifact(cfg,data);</span></span></span></div>
The error I get:</div>
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using ft_fetch_data</span>
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some of the requested samples occur twice in the data and have conflicting values</div>
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Error in ft_artifact_threshold (line 186)</div>
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dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));</div>
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Is there a way to adjust the cfg for ft_rejectartifact so that the function will accept that samples do indeed occur twice in the data and that the same sample can have different values in different trials (and data from the correct trial will be fetched)?</div>
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Here are a few solutions that I have tried based on other discussion list questions, that I have found to be unsatisfactory or ineffective:</div>
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<li style="list-style-type: disc;" class="">For ft_databrowser, it is possible to use cfg.allowoverlap = 'yes' to avoid errors due to conflicting sample values, but this setting is not available for ft_rejectartifact.</li><li style="list-style-type: disc;" class="">I do not want to remove or adjust the sampleinfo from the data, because I want to be able to relate trials to the original samples if necessary.</li><li style="list-style-type: disc;" class="">I have found that downsampling my signal will lead ft_rejectartifact to reconstruct the sampleinfo assuming that the trials are consecutive segments of a continuous recording, but I do not want to 'hack' my way around
the problem in this way.</li></ul>
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Hope you can help me out!</div>
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Best,</div>
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Maria</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 10pt;" class="">------------------------------------------------------------------------</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 10pt;" class="">Maria den Hartog, MSc | PhD Candidate | Radboud University </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 10pt;" class="">Centre for Language Studies | Grammar and Cognition<br class="">
Working days: Tuesday - Friday | Erasmus Building, Room 8.01</span></div>
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