[Mne_analysis] sLORETA

Pavan Ramkumar pavan at neuro.hut.fi
Thu Sep 1 12:34:45 EDT 2011
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Dear all,

As has been pointed out, both the Pascual-Marqui estimate (sLORETA) and
Dale's estimate (dSPM) normalize the MNE source estimate by the noise
estimate at each source point.

Slightly related issue. I have recently been trying to implement the
sLORETA noisenorm in Matlab. Sharing some lines of code to illustrate the
difference between dSPM and sLORETA estimates (I may be wrong):

%----------------------------------
%The common steps work as follows:
%----------------------------------
inv_op = mne_prepare_inverse_operator(inv_op, 1, 1/snr, 1);
inv_op.operator =
diag(sparse(sqrt(inv_op.source_cov.data)))*inv_op.eigen_leads.data*diag(sparse(inv_op.reginv))*inv_op.eigen_fields.data*inv_op.whitener*inv_op.proj;

% Extract the source covariance
R = diag(sparse(inv_op.source_cov.data));
% Whiten the forward solution
G = inv_op.whitener*fwd_op.sol.data;
% Whiten the noise covariance
% C is not necessarily an identity because of the projections and SSS
% (some entries are zero)
C = inv_op.whitener*inv_op.noise_cov.data*inv_op.whitener';

% Compute the inverse operator
inv_op.operator = R*G'*pinv(G*R*G' + 1/snr*C)*inv_op.whitener;
% Apply the inverse retaining only surface normal components
source = inv_op.operator(:,3:3:end)' * signal;

%---------------------
%dSPM works as follows:
%---------------------
% Apply the Dale noisenorm which has been precomputed in your inverse
operator structure inv_op
dSPMsource = inv_op.noisenorm * source;

%------------------------
%sLORETA works as follows:
%------------------------
% Compute the sloreta operator
for k=1:2*Ng
  inv_op.sloretanoisenorm{k}.data =
pinv(inv_op.operator2(3*k-2:3*k,:)*G(:,3*k-2:3*k));
end

% Apply the sLORETA noisenorm
for k=1:2*Ng
  sLORETAsource(k,:) =
source(3*k-2:3*k,:)'*inv_op.sloretanoisenorm{k}.data*source(3*k-2:3*k,:);

Kind regards,
Pavan

>> Yes.. the sLORETA solution scales the MNE by a factor that depends on
>> SNR
>> at each vertex. Thus it supresses noisy vertices a little. The MNE is
>> the
>> unscaled version which is in current units (say nano Amps) and hence you
>> can compare the left and right directly in a physiological sense.
>
> that can be problematic as MNE amplitudes are biased by the number of
> dipoles with the same forward field. Comparing MNE in one location between
> conditions is ok but comparing raw MNE between 2 brain regions is a
> problem.
>
> I would really do a z-score if it's any better than raw dSPM or sLORETA.
>
> Alex
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Pavan Ramkumar
Brain Research Unit
MEG Core
Low Temperature Laboratory
Aalto University School of Science
Espoo, Finland



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