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<font size="4" class="">Dear Xavier,</font>
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</font></div>
<div class=""><font size="4" class="">Thanks for your message. Let me forward your questions to the fieldtrip discussion list. If you haven’t signed up yet, please do so (<a href="http://www.fieldtriptoolbox.org/discussion_list/" class="">http://www.fieldtriptoolbox.org/discussion_list/</a>).</font></div>
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<div class=""><font size="4" class="">I prefer to have the interaction through the list, because then more people will benefit from the discussion. Also, other people who have an opinion about the questions can also chime in. Both points make the transfer of
knowledge more efficient.</font></div>
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<div class=""><font size="4" class="">At the moment, I don’t have much time to look in detail at your questions, since we are running our annual toolkit course at the Donders Centre right now (this year for the first time fully online). Therefore, I hope that
somebody reading this might pick up on your message.</font></div>
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<div class=""><font size="4" class="">Some quick pointers:</font></div>
<div class=""><font size="4" class="">1. It depends on the connectivity metric of interest, but for most I’d compute the source level data for the frequency filtered signals (assuming a beamformer). When you’d be using a distributed source modelling approach
(e.g. minimum norm estimate) the order probably doesn’t matter too much.</font></div>
<div class=""><font size="4" class="">2. No, 2 different measurements are likely too different (different electrode positions, SNR characteristics etc), so that appending them before the source reconstruction does not make sense.</font></div>
<div class=""><font size="4" class="">3. I did not check in detail, but your descriptions looks OK. This would be one way to get ‘parcellated’ results.</font></div>
<div class=""><font size="4" class="">4. In it’s ’naive’ (i.e. without additional settings) application the beamformer has a well-known ‘depth bias’, resulting in a large dynamic range of the amplitude of the dipoles, with dipole locations that are far away
from the sensors getting very large amplitudes. See <a href="http://www.fieldtriptoolbox.org/tutorial/beamformer/" class="">http://www.fieldtriptoolbox.org/tutorial/beamformer/</a> for another example (although it’s MEG, the same thing applies).</font></div>
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<div class=""><font size="4" class="">Best wishes,</font></div>
<div class=""><font size="4" class="">Jan-Mathijs</font></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Xavier Vrijdag <<a href="mailto:x.vrijdag@auckland.ac.nz" class="">x.vrijdag@auckland.ac.nz</a>><br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Source localisation mom results</b><br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">23 April 2020 at 02:12:02 CEST<br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>" <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
</span></div>
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<span lang="EN-US" style="" class="">Hello Jan-Mathijs,</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">I have been using fieldtrip for my EEG analysis for the last year and am really pleased with all the options the toolbox offers and the support given along my journey to understand how to use the toolbox. The documentation
on the website is really helpful to understand how to use the various parts of the toolbox.</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">So far I have programmed a preprocessing pipeline to clean my EEG data that I collected during exposures to various narcotic gases (resting state data). This data is fed into a source localization script with the ultimate
goal to do connectivity analysis (mutual information) and network analysis.</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">I have the following questions:</span><span style="" class=""><o:p class=""></o:p></span></div>
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<li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="EN-US" class="">Should I filter the EEG data into the standard frequency bands before the source localization, or is it better to filter the mom data that is fed into the connectivity analysis. With the goal to assess the connectivity in various
frequency bands</span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="EN-US" class="">Should I append the data from two measurements (separate days) for each participants or keep them separate during the source localization analysis (each measurement contains a baseline and exposure recording).</span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="EN-US" class="">Did I correctly use the parcellation functions to source-localize the data to the centroids of the 90 cortical regions?</span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></li><li class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="EN-US" class="">I intend to feed the mom field of the parcellated source struct into the connectivity analysis. I found that the range of the is 6.0571e+07. Is this correct/normal?</span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></li></ol>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">The script has the following steps (script file can be downloaded from:<a href="https://www.dropbox.com/s/jnf5dr56ytj543j/EEGsourselocalisationN2He.m?dl=0" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="color: rgb(4, 74, 145);" class="">https://www.dropbox.com/s/jnf5dr56ytj543j/EEGsourselocalisationN2He.m?dl=0</span></a>):</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">I currently have a source localization script that has the following steps:</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">I have a created a file with the aligned electrode locations</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">I use the standard BEM head model and the AAL atlas</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">create a 6 mm grid based leadfield</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">source interpolate the AAL atlas on the grid</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif; caret-color: rgb(0, 0, 0); font-variant-caps: normal; text-align: start; -webkit-text-stroke-width: 0px; word-spacing: 0px;" class="">
<span lang="EN-US" style="" class="">calculate the centroid position for each of the first 90 AAL regions</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">create new grid based on these center positions</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">new source interpolation of the AAL atlas on the new grid</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Append the baseline and exposure data</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Frequency band filter</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Calculate the channel covariance matrix for all exposures and for each exposure separately (keep trials)</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Calculate LCMV beamformer spatial filter on all exposure matrix</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Apply spatial filter and source parcellation on each exposure (keep trials and rawtrial)</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Thank you for helping me getting a better understanding of the source localization steps.</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Regards,</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class="">Xavier Vrijdag</span><span style="" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; color: rgb(51, 49, 49);" class="">Xavier Vrijdag, MSc</span><span style="" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; color: rgb(0, 55, 55);" class="">Researcher</span></b><span style="" class=""><o:p class=""></o:p></span></div>
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