[Mne_analysis] permutation cluster t-test for planar grads

Denis-Alexander Engemann denis.engemann at gmail.com
Thu Apr 14 09:49:17 EDT 2016
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I received a question with regard to my statement that gradiometers and
magnetometers get "fused" by SSS. So the reason why I say this is that the
covariance of the magnetometers and the gradiometers gets modified
dramatically, especially the cross-terms. Assume SSS of rank=64, the rank
of the mags and the grads is each 64 and the joint rank is also 64; both
are projections from the same SSS origin coordinate system. This gets more
obvious when computing whiteners from the covariance, the overall scaling
will be wrong if sensors are treated independently and with the correct
scaling / rank value one can see that magnetometers get dramatically
down-weighted and only marginally contribute to the overall RMS of the
whitened signal based on the grad+mag covariance. This is also the reason
why we auto-detect the presence of SSS and when showing
evoked.plot_white(covariance) only 1 signal for both mag + grad is shown
for SSSed data, while mags and grads are shown separately otherwise.
We figured out these details while implementing our advanced covariance
methods with Alex, Eric and Matti. From a point of view of the method all
this is not very surprising probably but certainly it remains implicit to
many.
I hope this makes the point a bit clearer.

Denis

On Wed, Apr 13, 2016 at 9:55 AM Lucy MacGregor <
Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:

> Hi Denis,
>
>
> Ah, thanks for the link.  I will take a look.
>
>
>
> Thanks again for the pointers.
>
>
>
> 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 09:30
>
>
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] permutation cluster t-test for planar grads
>
>
>
> 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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