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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Dear Silvia,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">What you could do is do your downsampling, re-referencing, filtering and ICA on continuous data and save the resulting
dataset as data1. Then, you do the artefact rejection on continuous data (unless you have long episodes that are of no interest, then you may reconsider) and save this to cfg_artifactrejection. That way, you obtain an artefact rejection file that is independent
from epoching, sometimes not the worst idea. Then you go back and load data1, do the epoching, and then do the artefact rejection.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Christine<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>Im Auftrag von </b>Silvia Formica<br>
<b>Gesendet:</b> Montag, 26. November 2018 16:12<br>
<b>An:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Betreff:</b> Re: [FieldTrip] ft_redefinedata after pre-processing<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Dear Christine,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">thank you for your quick response!<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">In my example <em><span style="font-family:"Calibri",sans-serif">data_cue</span></em> is epoched and pre-processed.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Nevertheless, I think the approach you suggested might work also in my case. I also downsample, re-reference and filter the continuous data. After these first steps, I epoch the cue-locked dataset.
After epoching, I perform artifact rejection and ICA.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I guess I can apply your approach to my data by running this exact same pipeline and saving the "cfg_artifactrejection" and my ICA components. Then I would go back to the filtered continuous data,
epoch them target-locked and apply to this target-locked dataset the <span style="background:white">"cfg_artifactrejection"</span> saved before and removing the same ICA components selected before.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Do you think this would be an acceptable approach?<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Thanks a lot!<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Silvia<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Blume Christine <<a href="mailto:christine.blume@sbg.ac.at">christine.blume@sbg.ac.at</a>><br>
<b>Sent:</b> 26 November 2018 15:43<br>
<b>To:</b> <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
<b>Subject:</b> Re: [FieldTrip] ft_redefinedata after pre-processing</span><span style="font-family:"Calibri",sans-serif;color:#212121">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#212121"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dear Silvia,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Do I understand correctly that
<i>data_cue</i> is epoched, but not pre-processed?</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">You can apply ft_rejectartifact after ft_redefinetrial. We usually pre-process continuous datasets and save the cfg of this pre-processing (in the
example below cfg_myartifactrejection). Only then we epoch the data and apply this artifactrejection.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">cfg=[];</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">cfg.trl=trl; # trl contains the trial definition of target-locked epochs</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">data_target = ft_redefinetrial (cfg, data_cue)</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">cfg = [];</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">data_target_clean = ft_rejectartifact(cfg_myartifactrejection, data_target);</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I hope this helps…</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Christine</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121">Von:</span></b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#212121"> fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>>
<b>Im Auftrag von </b>Silvia Formica<br>
<b>Gesendet:</b> Montag, 26. November 2018 14:19<br>
<b>An:</b> <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
<b>Betreff:</b> [FieldTrip] ft_redefinedata after pre-processing</span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Dear all,</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I'm in need of suggestions on the correct analyses strategy for my data.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I have an experiment with a cue followed (after ~2 seconds) by a target.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I epoched the data cue-locked and pre-processed my dataset. In my preprocessing I'm downsampling, re-referencing, rejecting some trials, running ICA, etc etc.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">My problem is that I would want to also epoch my data target-locked, but I want to do it after pre-processing the cue-locked dataset. This is because I want to exclude the same trials and apply exactly
the same corrections to the two different datasets.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I tried to use the function ft_redefinetrial, creating the new probe-locked trial definition and applying it to the cue-locked dataset.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">cfg=[];</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">cfg.trl=trl; # trl contains the trial definition of target-locked epochs</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">data_target = ft_redefinetrial (cfg, data_cue)</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">But I do not obtain what I wished for, because I get a data_target dataset that doesn't account for the trial rejection I performed while pre-processing the cue-locked dataset.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">So my questions are:</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">1) is it possible to achieve my goal?</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">2) If yes, what is the right strategy to do it?</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Thanks for any input and suggestion!</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Best,</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Silvia</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
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