<div dir="ltr">HI Maria, <div><br></div><div>the noise covariance is usually computed to take into account the correlation structure of the sensors, for example when computing an inverse solution.</div><div>As I understand the section you quoted it means that you cannot rely on naive SNR / or global field power measures computed from maxfilterered data since those are normalzied against the number of real number channels instead of the true rank of the data. The noiseocvariance however will reflect the rank of the max filtered rank data.</div>
<div><br></div><div>as an excercise you can compute the noise cov after maxfiltering the data and plot its eigenvalue spectra as demonstrated here: <a href="http://martinos.org/mne/stable/auto_examples/plot_estimate_covariance_matrix_baseline.html">http://martinos.org/mne/stable/auto_examples/plot_estimate_covariance_matrix_baseline.html</a></div>
<div><br></div><div>the kink in the plot should match the number of components estimated to be inside the head by maxfilter.</div><div><br></div><div>HTH,</div><div>Denis</div><div><br></div><div><br></div><div><br></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-08-26 17:46 GMT+02:00 Maria Hakonen <span dir="ltr"><<a href="mailto:maria.hakonen@gmail.com" target="_blank">maria.hakonen@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi all,</div><div><br></div><div>I have maxfiltered MEG data with the following arguments:</div><div>
<br></div><div>/neuro/bin/util/maxfilter -force -v -f "$subject"_"$file"_raw.fif -o "$subject"_"$file"_raw_tsss.fif -frame head -origin 0 0 50 \ -autobad 10000 -badlimit 7 -site biomag -st 16 -corr 0.95 > "$subject"_"$file"_maxfout</div>
<div><br></div><div>However, in Maxfilter manual it is said:</div><div><br></div><div>"Maxwell filtering however modifies the sensor noise properties, and the</div><div>baseline noises may become correlated. Therefore, statistical parameters</div>
<div>such as confidence intervals and volumes are incorrect if analysis software</div><div>uses sensor noises estimated from the baselines.</div><div><br></div><div>Note: Correlations of the sensor noises must be taken into account if the</div>
<div>Maxwell-filtered sensor noises are applied in source modelling."</div><div><br></div><div>I have calculated noise covariance matrixes from the baselines of Maxfiltered data using mne.compute_covariance. </div><div>
<br></div><div>Can these covariance matrixes be used in source modelling or how the noise covariances should be calculated if the data is Maxfiltered?</div><div><br></div><div>Any advice is welcome!</div><div><br></div><div>
Regards,</div><div>Maria</div></div>
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