mne.minimum_norm.make_inverse_operator

mne.minimum_norm.make_inverse_operator(info, forward, noise_cov, loose='auto', depth=0.8, fixed='auto', rank=None, use_cps=True, verbose=None)[source]

Assemble inverse operator.

Parameters
infodict

The measurement info to specify the channels to include. Bad channels in info[‘bads’] are not used.

forwarddict

Forward operator.

noise_covinstance of Covariance

The noise covariance matrix.

loosefloat | ‘auto’ | dict

Value that weights the source variances of the dipole components that are parallel (tangential) to the cortical surface. Can be:

  • float between 0 and 1 (inclusive)

    If 0, then the solution is computed with fixed orientation. If 1, it corresponds to free orientations.

  • 'auto' (default)

    Uses 0.2 for surface source spaces (unless fixed is True) and 1.0 for other source spaces (volume or mixed).

  • dict

    Mapping from the key for a given source space type (surface, volume, discrete) to the loose value. Useful mostly for mixed source spaces.

depthNone | float | dict

How to weight (or normalize) the forward using a depth prior. If float (default 0.8), it acts as the depth weighting exponent (exp) to use None is equivalent to 0, meaning no depth weighting is performed. It can also be a dict containing keyword arguments to pass to mne.forward.compute_depth_prior() (see docstring for details and defaults). This is effectively ignored when method='eLORETA'.

Changed in version 0.20: Depth bias ignored for method='eLORETA'.

fixedbool | ‘auto’

Use fixed source orientations normal to the cortical mantle. If True, the loose parameter must be “auto” or 0. If ‘auto’, the loose value is used.

rankNone | ‘info’ | ‘full’ | dict

This controls the rank computation that can be read from the measurement info or estimated from the data. When a noise covariance is used for whitening, this should reflect the rank of that covariance, otherwise amplification of noise components can occur in whitening (e.g., often during source localization).

None

The rank will be estimated from the data after proper scaling of different channel types.

'info'

The rank is inferred from info. If data have been processed with Maxwell filtering, the Maxwell filtering header is used. Otherwise, the channel counts themselves are used. In both cases, the number of projectors is subtracted from the (effective) number of channels in the data. For example, if Maxwell filtering reduces the rank to 68, with two projectors the returned value will be 66.

'full'

The rank is assumed to be full, i.e. equal to the number of good channels. If a Covariance is passed, this can make sense if it has been (possibly improperly) regularized without taking into account the true data rank.

dict

Calculate the rank only for a subset of channel types, and explicitly specify the rank for the remaining channel types. This can be extremely useful if you already know the rank of (part of) your data, for instance in case you have calculated it earlier.

This parameter must be a dictionary whose keys correspond to channel types in the data (e.g. 'meg', 'mag', 'grad', 'eeg'), and whose values are integers representing the respective ranks. For example, {'mag': 90, 'eeg': 45} will assume a rank of 90 and 45 for magnetometer data and EEG data, respectively.

The ranks for all channel types present in the data, but not specified in the dictionary will be estimated empirically. That is, if you passed a dataset containing magnetometer, gradiometer, and EEG data together with the dictionary from the previous example, only the gradiometer rank would be determined, while the specified magnetometer and EEG ranks would be taken for granted.

The default is None.

use_cpsbool

Whether to use cortical patch statistics to define normal orientations for surfaces (default True).

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). If used, it should be passed as a keyword-argument only.

Returns
invinstance of InverseOperator

Inverse operator.

Notes

For different sets of options (loose, depth, fixed) to work, the forward operator must have been loaded using a certain configuration (i.e., with force_fixed and surf_ori set appropriately). For example, given the desired inverse type (with representative choices of loose = 0.2 and depth = 0.8 shown in the table in various places, as these are the defaults for those parameters):

Inverse desired

Forward parameters allowed

loose

depth

fixed

force_fixed

surf_ori

Loose constraint,
Depth weighted

0.2

0.8

False

False

True

Loose constraint

0.2

None

False

False

True

Free orientation,
Depth weighted

1.0

0.8

False

False

True

Free orientation

1.0

None

False

False

True | False

Fixed constraint,
Depth weighted

0.0

0.8

True

False

True

Fixed constraint

0.0

None

True

True

True

Also note that, if the source space (as stored in the forward solution) has patch statistics computed, these are used to improve the depth weighting. Thus slightly different results are to be expected with and without this information.

For depth weighting, 0.8 is generally good for MEG, and between 2 and 5 is good for EEG, see 1.

References

1

Fa-Hsuan Lin, Thomas Witzel, Seppo P. Ahlfors, Steven M. Stufflebeam, John W. Belliveau, and Matti S. Hämäläinen. Assessing and improving the spatial accuracy in MEG source localization by depth-weighted minimum-norm estimates. NeuroImage, 31(1):160–171, May 2006. doi:10.1016/j.neuroimage.2005.11.054.

Examples using mne.minimum_norm.make_inverse_operator