[Mne_analysis] permutation cluster t-test for planar grads

Denis-Alexander Engemann denis.engemann at gmail.com
Tue Apr 12 10:18:18 EDT 2016
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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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