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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Hi Denis,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Thanks for confirming my understanding of how the templates are used.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Wrt to the creating virtual magnetometers using the channel remapping method, what do you mean when you say it would have the advantage of keeping a more interpretable
signal?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Lucy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mne_analysis-bounces@nmr.mgh.harvard.edu [mailto:mne_analysis-bounces@nmr.mgh.harvard.edu]
<b>On Behalf Of </b>Denis-Alexander Engemann<br>
<b>Sent:</b> 13 April 2016 09:11<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] permutation cluster t-test for planar grads<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Lucy,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">yes you're absolutely conceptualizing it. The neighbour definitions are simply telling the naive statistical procedures which variables should be considered neighbours, hence, potentially grouped in a cluster.<o:p></o:p></p>
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<p class="MsoNormal">But should you use SSS keep in mind that grads and mags are not independent. If you still observe different effects this is to some extent arbitrary.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Denis<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">On Wed, Apr 13, 2016 at 8:58 AM Lucy MacGregor <<a href="mailto:Lucy.MacGregor@mrc-cbu.cam.ac.uk">Lucy.MacGregor@mrc-cbu.cam.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Hi Denis,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Thank you for the reply. Since I want to analyse magnetometers and gradiometers separately I will
go ahead and use the magnetometer neighbour connectivity for the moment. Am I correct in thinking that there should be no adverse effects on any scaling (grads and mags are obviously in different units) because all the neighbour connectivity does is provide
a layout of channel positions/neighbours?<br>
<br>
Thanks for drawing my attention to the channel remapping.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Lucy</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a> [mailto:<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>]
<b>On Behalf Of </b>Denis-Alexander Engemann<br>
<b>Sent:</b> 12 April 2016 15:18<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] permutation cluster t-test for planar grads</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Lucy,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">as far as I see it there aren't any templates available for merged gradiometers. You could probably do what you describe as all sensors are anyways organized in triplets, the magnetometer
neighbor connectivity should therefore be enough. We also have a channel remapping method in the evoked object but it I am not sure up to which extent it can be used beyond illustrative contexts. Here you would create virtual magnetometers, which would have
the advantage that you keep a more interpretable signal. If you have used SSS you might also consider just using the magnetometers, as SSS, so to say, fuses magnetometers and gradiometers. In other words after SSS they are not any longer independent but provide
alternative views on the same underlying structure with something between 64 and 90 linearly independent dimensions.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I hope this helps a bit.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Denis<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Apr 12, 2016 at 2:28 PM Lucy MacGregor <<a href="mailto:Lucy.MacGregor@mrc-cbu.cam.ac.uk" target="_blank">Lucy.MacGregor@mrc-cbu.cam.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Dear MNE users,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">I wish to run permutation cluster t-test (2-tailed) on my sensor level data (cond A vs. cond B). I am wondering
how best to deal with the planar gradiometer data from a Neuromag 306 system and would be grateful for advice.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Since I am not interested in the direction of the gradients at individual gradiometers within a pair, I think it
makes most sense to combine the data for each 102 pairs using RMS (for each gradiometer then RMS</span>(<strong><span style="font-family:"Calibri","sans-serif"">g</span></strong>) = sqrt(sum(g<span style="font-family:"Cambria Math","serif"">₁</span>²+g<span style="font-family:"Cambria Math","serif"">₂</span>²)/2)).
I would perform the t-tests on these RMS data. I then wondered how neighbourhood definitions for clustering ought to be defined – I was thinking I could replace my magnetometer values with the new RMS gradiometer values and use the neighbourhood definitions
from “neuromag306mag”. <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I took the options for the neighbourhood templates after reading this page here:<br>
<a href="http://martinos.org/mne/dev/generated/mne.channels.read_ch_connectivity.html#mne.channels.read_ch_connectivity" target="_blank">http://martinos.org/mne/dev/generated/mne.channels.read_ch_connectivity.html#mne.channels.read_ch_connectivity</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Does this make sense or would you suggest a different approach? Ought I to obtain t-values for each of the 204 gradiometers and perform the clustering on these values instead?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Many thanks for any guidance,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Lucy MacGregor</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#A6A6A6">******************************************************************</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#A6A6A6">Lucy MacGregor</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#A6A6A6">MRC Cognition and Brain Sciences Unit</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";color:#A6A6A6">15 Chaucer Road</span><o:p></o:p></p>
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