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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear all,
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<div>I want to do SAM beamformer source localization on single trial EEG data. I would like to normalize the leadfields to correct for depth, like mentioned in the lmcv beamformer tutorial: (http://www.fieldtriptoolbox.org/tutorial/beamformer_lcmv)</div>
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<div><font face="Courier New">cfg = [];</font></div>
<div><font face="Courier New">cfg.elec = hdr.elec; % electrode distances</font></div>
<div><font face="Courier New">cfg.headmodel = vol; % volume conduction headmodel</font></div>
<div><font face="Courier New">cfg.grid = grid; % normalized grid positions</font></div>
<div><font face="Courier New">cfg.channel = {'EEG'};</font></div>
<div><font face="Courier New">cfg.normalize = 'yes'; % to remove depth bias (Q in eq. 27 of van Veen et al, 1997). </font></div>
<div><font face="Courier New">lf = ft_prepare_leadfield(cfg);</font></div>
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<div>However when I look what happens with cfg.normalize='yes', the following script is used in ft_compute_leadfield, from line 570:</div>
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<div><font face="Courier New"> case 'yes'</font></div>
<div><font face="Courier New"> for ii=1:Ndipoles</font></div>
<div><font face="Courier New"> tmplf = lf(:, (3*ii-2):(3*ii));</font></div>
<div><font face="Courier New"> if normalizeparam==0.5</font></div>
<div><font face="Courier New"> % normalize the leadfield by the Frobenius norm of the matrix</font></div>
<div><font face="Courier New"> % this is the same as below in case normalizeparam is 0.5</font></div>
<div><font face="Courier New"> nrm = norm(tmplf, 'fro');</font></div>
<div><font face="Courier New"> else</font></div>
<div><font face="Courier New"> % normalize the leadfield by sum of squares of the elements of the leadfield matrix to the power "normalizeparam"</font></div>
<div><font face="Courier New"> % this is the same as the Frobenius norm if normalizeparam is 0.5</font></div>
<div><font face="Courier New"> nrm = sum(tmplf(:).^2)^normalizeparam;</font></div>
<div><font face="Courier New"> end</font></div>
<div><font face="Courier New"> if nrm>0</font></div>
<div><font face="Courier New"> tmplf = tmplf ./ nrm;</font></div>
<div><font face="Courier New"> end</font></div>
<div><font face="Courier New"> lf(:, (3*ii-2):(3*ii)) = tmplf;</font></div>
<div><font face="Courier New"> end</font></div>
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<div>This seems to me as independent of the dipole location, and does not use an estimate of the noise spectrum as in Eq 27 of van Veen et al 1997. </div>
<div>DICS beamformer has the option to estimate the noise spectrum with 'projectnoise', but SAM beamformer does not have that option. SAM does something with noise and a lambda, which is noise regularization I guess (beamformer_sam from line 102). <span style="font-size: 13.3333px;">I
use Fieldtrip 20170212.</span></div>
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<div>My main question: how do I correct the leadfields for depth bias?</div>
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<div>Thanks in advance,</div>
<div>Nicole</div>
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