[Mne_analysis] permutation cluster t-test for planar grads

[Denis-Alexander Engemann]

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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