[Mne_analysis] permutation cluster t-test for planar grads

Denis-Alexander Engemann denis.engemann at gmail.com
Wed Apr 13 04:30:10 EDT 2016
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Hi Lucy,

it means that you transform the gradiometers such that the result has
n_channels/2 signals that look like magnetometer signals.

Also see here:
http://martinos.org/mne/dev/auto_examples/preprocessing/plot_virtual_evoked.html

Denis

On Wed, Apr 13, 2016 at 9:25 AM Lucy MacGregor <
Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:

> Hi Denis,
>
>
>
> Thanks for confirming my understanding of how the templates are used.
>
>
>
> 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?
>
>
>
> Lucy
>
>
>
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:
> mne_analysis-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Denis-Alexander
> Engemann
> *Sent:* 13 April 2016 09:11
>
>
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] permutation cluster t-test for planar grads
>
>
>
> Hi Lucy,
>
>
>
> 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.
>
> 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.
>
>
>
> Denis
>
>
>
>
>
> On Wed, Apr 13, 2016 at 8:58 AM Lucy MacGregor <
> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>
> Hi Denis,
>
>
>
> 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?
>
> Thanks for drawing my attention to the channel remapping.
>
>
>
> Lucy
>
>
>
>
>
>
>
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:
> mne_analysis-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Denis-Alexander
> Engemann
> *Sent:* 12 April 2016 15:18
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] permutation cluster t-test for planar grads
>
>
>
> Hi Lucy,
>
>
>
> 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.
>
>
>
> I hope this helps a bit.
>
> Denis
>
>
>
>
>
> On Tue, Apr 12, 2016 at 2:28 PM Lucy MacGregor <
> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>
> Dear MNE users,
>
>
>
> 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.
>
>
>
> 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(*g*) =
> sqrt(sum(g₁²+g₂²)/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”.
>
>
>
> I took the options for the neighbourhood templates after reading this page
> here:
>
> http://martinos.org/mne/dev/generated/mne.channels.read_ch_connectivity.html#mne.channels.read_ch_connectivity
>
>
>
>
>
> 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?
>
>
>
> Many thanks for any guidance,
>
>
>
> Lucy MacGregor
>
>
>
> ******************************************************************
>
> Lucy MacGregor
>
> MRC Cognition and Brain Sciences Unit
>
> 15 Chaucer Road
>
> Cambridge CB2 7EF
>
> Tel: 01223 355294 Ext 860
>
> http://www.mrc-cbu.cam.ac.uk/people/lucy.macgregor/
>
>
>
>
>
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