How to get noise covariances if data is Maxfiltered

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1

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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2

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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3

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

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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