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

[Maria Hakonen]

Many thanks Denis!
I will try this example.

-Maria


2014-08-26 18:52 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

> HI Maria,
>
> the noise covariance is usually computed to take into account the
> correlation structure of the sensors, for example when computing an inverse
> solution.
> 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.
>
> as an excercise you can compute the noise cov after maxfiltering the data
> and plot its eigenvalue spectra as demonstrated here:
> http://martinos.org/mne/stable/auto_examples/plot_estimate_covariance_matrix_baseline.html
>
> the kink in the plot should match the number of components estimated to be
> inside the head by maxfilter.
>
> HTH,
> Denis
>
>
>
>
>
> 2014-08-26 17:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:
>
>> 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
>>
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