mne.compute_raw_covariance

mne.compute_raw_covariance(raw, tmin=0, tmax=None, tstep=0.2, reject=None, flat=None, picks=None, method='empirical', method_params=None, cv=3, scalings=None, n_jobs=1, return_estimators=False, verbose=None)

Estimate noise covariance matrix from a continuous segment of raw data.

It is typically useful to estimate a noise covariance from empty room data or time intervals before starting the stimulation.

Note

This function will:

  1. Partition the data into evenly spaced, equal-length epochs.
  2. Load them into memory.
  3. Subtract the mean across all time points and epochs for each channel.
  4. Process the Epochs by compute_covariance().

This will produce a slightly different result compared to using make_fixed_length_events(), Epochs, and compute_covariance() directly, since that would (with the recommended baseline correction) subtract the mean across time for each epoch (instead of across epochs) for each channel.

Parameters:

raw : instance of Raw

Raw data

tmin : float

Beginning of time interval in seconds. Defaults to 0.

tmax : float | None (default None)

End of time interval in seconds. If None (default), use the end of the recording.

tstep : float (default 0.2)

Length of data chunks for artefact rejection in seconds. Can also be None to use a single epoch of (tmax - tmin) duration. This can use a lot of memory for large Raw instances.

reject : dict | None (default None)

Rejection parameters based on peak-to-peak amplitude. Valid keys are ‘grad’ | ‘mag’ | ‘eeg’ | ‘eog’ | ‘ecg’. If reject is None then no rejection is done. Example:

reject = dict(grad=4000e-13, # T / m (gradiometers)
              mag=4e-12, # T (magnetometers)
              eeg=40e-6, # V (EEG channels)
              eog=250e-6 # V (EOG channels)
              )

flat : dict | None (default None)

Rejection parameters based on flatness of signal. Valid keys are ‘grad’ | ‘mag’ | ‘eeg’ | ‘eog’ | ‘ecg’, and values are floats that set the minimum acceptable peak-to-peak amplitude. If flat is None then no rejection is done.

picks : array-like of int | None (default None)

Indices of channels to include (if None, data channels are used).

method : str | list | None (default ‘empirical’)

The method used for covariance estimation. See mne.compute_covariance().

New in version 0.12.

method_params : dict | None (default None)

Additional parameters to the estimation procedure. See mne.compute_covariance().

New in version 0.12.

cv : int | sklearn cross_validation object (default 3)

The cross validation method. Defaults to 3, which will internally trigger a default 3-fold shuffle split.

New in version 0.12.

scalings : dict | None (default None)

Defaults to dict(mag=1e15, grad=1e13, eeg=1e6). These defaults will scale magnetometers and gradiometers at the same unit.

New in version 0.12.

n_jobs : int (default 1)

Number of jobs to run in parallel.

New in version 0.12.

return_estimators : bool (default False)

Whether to return all estimators or the best. Only considered if method equals ‘auto’ or is a list of str. Defaults to False

New in version 0.12.

verbose : bool | str | int | None (default None)

If not None, override default verbose level (see mne.verbose).
Returns:

cov : instance of Covariance | list

The computed covariance. If method equals ‘auto’ or is a list of str and return_estimators equals True, a list of covariance estimators is returned (sorted by log-likelihood, from high to low, i.e. from best to worst).

See also

compute_covariance
Estimate noise covariance matrix from epochs