[Mne_analysis] [Freesurfer] question about how to calculate COV for MNE

[dgw]

Hi Joe,

I have forwarded your email to the mne_analysis list (please
subscribe). This is the list for MNE questions. Does anyone have the
answers for Joe?


HTH,
D

On Fri, Apr 4, 2014 at 10:50 AM, Joseph Dien <jdien07 at mac.com> wrote:
> Hi,
>    I have a question about how to calculate the COV for the MNE software.
> As I understand it from Section 4.17 of the 2.7.3 MNE manual, if one is
> averaging together COV matrices, one weights them by the number of
> observations going into each one.  I also see from Section 4.17.2 that these
> are technically not covariance matrices so much as sum-of-squares matrices
> where the epochs going into each variable has been baseline corrected.
>
>    Assuming my understanding so far is correct, my question is about how to
> proceed when making linear combinations of COV matrices, as in a difference
> wave, as discussed in Section 6.3.  Would the following be the correct
> procedure?
>
>    Compute the COV separately for the two conditions (say standard and rare
> oddballs).  Subtract the two COV matrices to obtain C0. Then calculate C by
> dividing by Leff, which in turn is calculated as Leff= (L1*L2)/(L1+L2) where
> L1 is the number of observations in the first COV matrix and L2 is for the
> second.
>
>    But if done in this way, the two COV matrices would not be weighted by
> their relative sample sizes.  So would I also weight them by L1 and L2
> during the subtraction, as done for averaging per 4.17?  But then what is
> the purpose of the Leff calculation? Or is the idea that one would calculate
> a single COV based on both conditions and then one would modify COV by Leff
> to reflect that the signal-to-noise ratio has been reduced by combining two
> averages with differing sample sizes?  But in the case where both samples
> equal, say, 10, Leff would end up equalling 100/20=5.  Dividing C by 5 seems
> like too much.  Anyway, very confused.  Any guidance would be appreciated.
>
> Respectfully,
>
> Joe
>
>
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland
>
> E-mail: jdien07 at mac.com
> Phone: 202-297-8117
> http://joedien.com
>
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