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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Hi Sara,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">The electrodes and the MRI will be aligned when both are in the same coordinate system that is based on 3 points (the so called fiducials).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">You can define the fiducials for your MRI manually using ft_volumerealign with cfg.method = ‘interactive’.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">EEG systems typically do not include an integrated way to record and store EEG electrode locations and fiducials. A method to define fiducials and
electrode locations is using a 3D scanner and the function ft_electrodeplacement (see:
<a href="https://www.fieldtriptoolbox.org/tutorial/electrode/#loading-the-data-and-coregistration">
https://www.fieldtriptoolbox.org/tutorial/electrode/#loading-the-data-and-coregistration</a>).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Also, even though I have not used it myself I believe that you can use ft_electroderealign (with the cfg.method of your choice) to realign the electrodes
with the head surface (or headshape) generated from the MRI. In that case you need to take some steps before that, i.e. you need to realign your MRI (ft_volumerealign – which I mentioned in the first paragraph), segment the MRI (ft_volumesegment) and create
a head model (ft_prepare_headmodel). The head surface is stored in vol.bnd<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">(see:
<a href="https://www.fieldtriptoolbox.org/example/electrodes2bem/">https://www.fieldtriptoolbox.org/example/electrodes2bem/</a>)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Konstantinos<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Sara Cinelli via fieldtrip<br>
<b>Sent:</b> Monday, July 15, 2024 2:11 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> Sara Cinelli <sara.cinelli@studenti.unipd.it><br>
<b>Subject:</b> [FieldTrip] ft_electroderealign<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Hello, I'm going to explain my problem regarding the source reconstruction.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">How can I realigned the electrode placement with the mesh from the MRI? I tried using the function ft_electrode_realign using the following settings:</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.method =
<span style="color:#A709F5">'interactive';</span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.headshape = mesh;
</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">elec_realigned = ft_electroderealign(cfg, elec);</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">My first question is : can I do this having two differents coordinates for the mri and the eeg structure? If not, what sould I do before the realignment? My interest is the have the same coordinates
system of the mri image. </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Otherwise, the way I explained here is one with the interactive option, how can I understand which transformation to apply (only visually?)? I saw there could be another option, maybe with the
specification of the fiducials from the mri image, but it is not very clear to me how to use it. </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Thank you for helping me,</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Sara</span><o:p></o:p></p>
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