[Mne_analysis] How to get noise covariances if data is Maxfiltered

[Maria Hakonen]

Hi all,

I have maxfiltered MEG data with the following arguments:

/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

However, in Maxfilter manual it is said:

"Maxwell filtering however modifies the sensor noise properties, and the
baseline noises may become correlated. Therefore, statistical parameters
such as confidence intervals and volumes are incorrect if analysis software
uses sensor noises estimated from the baselines.

Note: Correlations of the sensor noises must be taken into account if the
Maxwell-filtered sensor noises are applied in source modelling."

I have calculated noise covariance matrixes from the baselines of
Maxfiltered data using mne.compute_covariance.

Can these covariance matrixes be used in source modelling or how the noise
covariances should be calculated if the data is Maxfiltered?

Any advice is welcome!

Regards,
Maria
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140826/9c05cf67/attachment.html