Contents

This page describes the mathematical concepts and the
computation of the minimum-norm estimates.
Using the UNIX commands this is accomplished with two programs:
mne_inverse_operator and mne_make_movie or in Python
using `mne.minimum_norm.make_inverse_operator()`

and the `apply`

functions. The use of these functions is
presented in the tutorial Source localization with MNE/dSPM/sLORETA.

The page starts with a mathematical description of the method. The interactive program for inspecting data and inverse solutions, mne_analyze, is covered in Interactive analysis with mne_analyze.

This section describes the mathematical details of the calculation of minimum-norm estimates. In Bayesian sense, the ensuing current distribution is the maximum a posteriori (MAP) estimate under the following assumptions:

- The viable locations of the currents are constrained to the cortex. Optionally, the current orientations can be fixed to be normal to the cortical mantle.
- The amplitudes of the currents have a Gaussian prior distribution with a known source covariance matrix.
- The measured data contain additive noise with a Gaussian distribution with a known covariance matrix. The noise is not correlated over time.

The measured data in the source estimation procedure consists of MEG and EEG data, recorded on a total of N channels. The task is to estimate a total of M strengths of sources located on the cortical mantle. If the number of source locations is P, M = P for fixed-orientation sources and M = 3P if the source orientations are unconstrained. The regularized linear inverse operator following from the Bayesian approach is given by the \(M \times N\) matrix

\[M = R' G^T (G R' G^T + C)^{-1}\ ,\]

where G is the gain matrix relating the source strengths to the measured MEG/EEG data, \(C\) is the data noise-covariance matrix and \(R'\) is the source covariance matrix. The dimensions of these matrices are \(N \times M\), \(N \times N\), and \(M \times M\), respectively. The \(M \times 1\) source-strength vector is obtained by multiplying the \(N \times 1\) data vector by \(M\).

The expected value of the current amplitudes at time *t* is
then given by \(\hat{j}(t) = Mx(t)\), where \(x(t)\) is
a vector containing the measured MEG and EEG data values at time *t*.

The a priori variance of the currents is, in practise, unknown. We can express this by writing \(R' = R/ \lambda^2\), which yields the inverse operator

\[M = R G^T (G R G^T + \lambda^2 C)^{-1}\ ,\]

where the unknown current amplitude is now interpreted in terms of the regularization parameter \(\lambda^2\). Small \(\lambda^2\) corresponds to large current amplitudes and complex estimate current patterns while a large \(\lambda^2\) means the amplitude of the current is limited and a simpler, smooth, current estimate is obtained.

We can arrive in the regularized linear inverse operator also by minimizing the cost function

\[S = \tilde{e}^T \tilde{e} + \lambda^2 j^T R^{-1} j\ ,\]

where the first term consists of the difference between the whitened measured data (see Whitening and scaling) and those predicted by the model while the second term is a weighted-norm of the current estimate. It is seen that, with increasing \(\lambda^2\), the source term receive more weight and larger discrepancy between the measured and predicted data is tolerable.

The MNE software employs data whitening so that a ‘whitened’ inverse operator assumes the form

\[\tilde{M} = R \tilde{G}^T (\tilde{G} R \tilde{G}^T + I)^{-1}\ ,\]

where \(\tilde{G} = C^{-^1/_2}G\) is the spatially
whitened gain matrix. The expected current values are \(\hat{j} = Mx(t)\),
where \(x(t) = C^{-^1/_2}x(t)\) is a the whitened measurement
vector at *t*. The spatial whitening operator
is obtained with the help of the eigenvalue decomposition \(C = U_C \Lambda_C^2 U_C^T\) as \(C^{-^1/_2} = \Lambda_C^{-1} U_C^T\).
In the MNE software the noise-covariance matrix is stored as the
one applying to raw data. To reflect the decrease of noise due to
averaging, this matrix, \(C_0\), is scaled
by the number of averages, \(L\), *i.e.*, \(C = C_0 / L\).

As shown above, regularization of the inverse solution is
equivalent to a change in the variance of the current amplitudes
in the Bayesian *a priori* distribution.

Convenient choice for the source-covariance matrix \(R\) is such that \(\text{trace}(\tilde{G} R \tilde{G}^T) / \text{trace}(I) = 1\). With this choice we can approximate \(\lambda^2 \sim 1/SNR\), where SNR is the (power) signal-to-noise ratio of the whitened data.

Note

The definition of the signal to noise-ratio/ \(\lambda^2\) relationship given above works nicely for the whitened forward solution. In the un-whitened case scaling with the trace ratio \(\text{trace}(GRG^T) / \text{trace}(C)\) does not make sense, since the diagonal elements summed have, in general, different units of measure. For example, the MEG data are expressed in T or T/m whereas the unit of EEG is Volts.

See Computing covariance matrix for example of noise covariance computation and whitening.

Since finite amount of data is usually available to compute an estimate of the noise-covariance matrix \(C\), the smallest eigenvalues of its estimate are usually inaccurate and smaller than the true eigenvalues. Depending on the seriousness of this problem, the following quantities can be affected:

- The model data predicted by the current estimate,
- Estimates of signal-to-noise ratios, which lead to estimates of the required regularization, see Regularization,
- The estimated current values, and
- The noise-normalized estimates, see Noise normalization.

Fortunately, the latter two are least likely to be affected
due to regularization of the estimates. However, in some cases especially
the EEG part of the noise-covariance matrix estimate can be deficient, *i.e.*,
it may possess very small eigenvalues and thus regularization of
the noise-covariance matrix is advisable.

Historically, the MNE software accomplishes the regularization by replacing a noise-covariance matrix estimate \(C\) with

\[C' = C + \sum_k {\varepsilon_k \bar{\sigma_k}^2 I^{(k)}}\ ,\]

where the index \(k\) goes across the different channel groups (MEG planar gradiometers, MEG axial gradiometers and magnetometers, and EEG), \(\varepsilon_k\) are the corresponding regularization factors, \(\bar{\sigma_k}\) are the average variances across the channel groups, and \(I^{(k)}\) are diagonal matrices containing ones at the positions corresponding to the channels contained in each channel group.

Using the UNIX tools mne_inverse_operator, the values
\(\varepsilon_k\) can be adjusted with the regularization options
`--magreg`

, `--gradreg`

, and `--eegreg`

specified at the time of the
inverse operator decomposition, see Inverse-operator decomposition. The convenience script
mne_do_inverse_operator has the `--magreg`

and `--gradreg`

combined to
a single option, `--megreg`

, see Calculating the inverse operator.
Suggested range of values for \(\varepsilon_k\) is \(0.05 \dotso 0.2\).

The most straightforward approach to calculate the MNE is to employ expression for the original or whitened inverse operator directly. However, for computational convenience we prefer to take another route, which employs the singular-value decomposition (SVD) of the matrix

\[A = \tilde{G} R^{^1/_2} = U \Lambda V^T\]

where the superscript \(^1/_2\) indicates a square root of \(R\). For a diagonal matrix, one simply takes the square root of \(R\) while in the more general case one can use the Cholesky factorization \(R = R_C R_C^T\) and thus \(R^{^1/_2} = R_C\).

With the above SVD it is easy to show that

\[\tilde{M} = R^{^1/_2} V \Gamma U^T\]

where the elements of the diagonal matrix \(\Gamma\) are

\[\gamma_k = \frac{1}{\lambda_k} \frac{\lambda_k^2}{\lambda_k^2 + \lambda^2}\ .\]

With \(w(t) = U^T C^{-^1/_2} x(t)\) the expression for the expected current is

\[\hat{j}(t) = R^C V \Gamma w(t) = \sum_k {\bar{v_k} \gamma_k w_k(t)}\ ,\]

where \(\bar{v_k} = R^C v_k\), \(v_k\) being the \(k\) th column of \(V\). It is thus seen that the current estimate is a weighted sum of the ‘modified’ eigenleads \(v_k\).

It is easy to see that \(w(t) \propto \sqrt{L}\). To maintain the relation \((\tilde{G} R \tilde{G}^T) / \text{trace}(I) = 1\) when \(L\) changes we must have \(R \propto 1/L\). With this approach, \(\lambda_k\) is independent of \(L\) and, for fixed \(\lambda\), we see directly that \(j(t)\) is independent of \(L\).

The noise-normalized linear estimates introduced by Dale et al. require division of the expected current amplitude by its variance. Noise normalization serves three purposes:

- It converts the expected current value into a dimensionless statistical test variable. Thus the resulting time and location dependent values are often referred to as dynamic statistical parameter maps (dSPM).
- It reduces the location bias of the estimates. In particular, the tendency of the MNE to prefer superficial currents is eliminated.
- The width of the point-spread function becomes less dependent on the source location on the cortical mantle. The point-spread is defined as the MNE resulting from the signals coming from a point current source (a current dipole) located at a certain point on the cortex.

In practice, noise normalization requires the computation of the diagonal elements of the matrix

\[M C M^T = \tilde{M} \tilde{M}^T\ .\]

With help of the singular-value decomposition approach we see directly that

\[\tilde{M} \tilde{M}^T\ = \bar{V} \Gamma^2 \bar{V}^T\ .\]

Under the conditions expressed at the end of Computation of the solution, it follows that the *t*-statistic values associated
with fixed-orientation sources) are thus proportional to \(\sqrt{L}\) while
the *F*-statistic employed with free-orientation sources is proportional
to \(L\), correspondingly.

Note

A section discussing statistical considerations related to the noise normalization procedure will be added to this manual in one of the subsequent releases.

Note

The MNE software usually computes the square roots of the F-statistic to be displayed on the inflated cortical surfaces. These are also proportional to \(\sqrt{L}\).

Under noiseless conditions the SNR is infinite and thus leads to \(\lambda^2 = 0\) and the minimum-norm estimate explains the measured data perfectly. Under realistic conditions, however, \(\lambda^2 > 0\) and there is a misfit between measured data and those predicted by the MNE. Comparison of the predicted data, here denoted by \(x(t)\), and measured one can give valuable insight on the correctness of the regularization applied.

In the SVD approach we easily find

\[\hat{x}(t) = G \hat{j}(t) = C^{^1/_2} U \Pi w(t)\ ,\]

where the diagonal matrix \(\Pi\) has elements \(\pi_k = \lambda_k \gamma_k\) The predicted data is thus expressed as the weighted sum of the ‘recolored eigenfields’ in \(C^{^1/_2} U\).

If the `--cps`

option was used in source space
creation (see Setting up the source space) or if mne_add_patch_info described
in mne_add_patch_info was run manually the source space file
will contain for each vertex of the cortical surface the information
about the source space point closest to it as well as the distance
from the vertex to this source space point. The vertices for which
a given source space point is the nearest one define the cortical
patch associated with with the source space point. Once these data
are available, it is straightforward to compute the following cortical
patch statistics (CPS) for each source location \(d\):

- The average over the normals of at the vertices in a patch, \(\bar{n_d}\),
- The areas of the patches, \(A_d\), and
- The average deviation of the vertex normals in a patch from their average, \(\sigma_d\), given in degrees.

The principal sources of MEG and EEG signals are generally believed to be postsynaptic currents in the cortical pyramidal neurons. Since the net primary current associated with these microscopic events is oriented normal to the cortical mantle, it is reasonable to use the cortical normal orientation as a constraint in source estimation. In addition to allowing completely free source orientations, the MNE software implements three orientation constraints based of the surface normal data:

- Source orientation can be rigidly fixed
to the surface normal direction (the
`--fixed`

option). If cortical patch statistics are available the average normal over each patch, \(\bar{n_d}\), are used to define the source orientation. Otherwise, the vertex normal at the source space location is employed. - A
*location independent or fixed loose orientation constraint*(fLOC) can be employed (the`--loose`

option). In this approach, a source coordinate system based on the local surface orientation at the source location is employed. By default, the three columns of the gain matrix G, associated with a given source location, are the fields of unit dipoles pointing to the directions of the x, y, and z axis of the coordinate system employed in the forward calculation (usually the MEG head coordinate frame). For LOC the orientation is changed so that the first two source components lie in the plane normal to the surface normal at the source location and the third component is aligned with it. Thereafter, the variance of the source components tangential to the cortical surface are reduced by a factor defined by the`--loose`

option. - A
*variable loose orientation constraint*(vLOC) can be employed (the`--loosevar`

option). This is similar to fLOC except that the value given with the`--loosevar`

option will be multiplied by \(\sigma_d\), defined above.

The minimum-norm estimates have a bias towards superficial currents. This tendency can be alleviated by adjusting the source covariance matrix \(R\) to favor deeper source locations. In the depth weighting scheme employed in MNE analyze, the elements of \(R\) corresponding to the \(p\) th source location are be scaled by a factor

\[f_p = (g_{1p}^T g_{1p} + g_{2p}^T g_{2p} + g_{3p}^T g_{3p})^{-\gamma}\ ,\]

where \(g_{1p}\), \(g_{2p}\), and \(g_{3p}\) are the three columns
of \(G\) corresponding to source location \(p\) and \(\gamma\) is
the order of the depth weighting, specified with the `--weightexp`

option
to mne_inverse_operator . The
maximal amount of depth weighting can be adjusted `--weightlimit`

option.

The fMRI weighting in MNE software means that the source-covariance matrix
is modified to favor areas of significant fMRI activation. For this purpose,
the fMRI activation map is thresholded first at the value defined by
the `--fmrithresh`

option to mne_do_inverse_operator or mne_inverse_operator .
Thereafter, the source-covariance matrix values corresponding to
the the sites under the threshold are multiplied by \(f_{off}\), set
by the `--fmrioff`

option.

It turns out that the fMRI weighting has a strong influence on the MNE but the noise-normalized estimates are much less affected by it.

It is often the case that the epoch to be analyzed is a linear combination over conditions rather than one of the original averages computed. As stated above, the noise-covariance matrix computed is originally one corresponding to raw data. Therefore, it has to be scaled correctly to correspond to the actual or effective number of epochs in the condition to be analyzed. In general, we have

\[C = C_0 / L_{eff}\]

where \(L_{eff}\) is the effective number of averages. To calculate \(L_{eff}\) for an arbitrary linear combination of conditions

\[y(t) = \sum_{i = 1}^n {w_i x_i(t)}\]

we make use of the the fact that the noise-covariance matrix

\[C_y = \sum_{i = 1}^n {w_i^2 C_{x_i}} = C_0 \sum_{i = 1}^n {w_i^2 / L_i}\]

which leads to

\[1 / L_{eff} = \sum_{i = 1}^n {w_i^2 / L_i}\]

An important special case of the above is a weighted average, where

\[w_i = L_i / \sum_{i = 1}^n {L_i}\]

and, therefore

\[L_{eff} = \sum_{i = 1}^n {L_i}\]

Instead of a weighted average, one often computes a weighted sum, a simplest case being a difference or sum of two categories. For a difference \(w_1 = 1\) and \(w_2 = -1\) and thus

\[1 / L_{eff} = 1 / L_1 + 1 / L_2\]

or

\[L_{eff} = \frac{L_1 L_2}{L_1 + L_2}\]

Interestingly, the same holds for a sum, where \(w_1 = w_2 = 1\). Generalizing, for any combination of sums and differences, where \(w_i = 1\) or \(w_i = -1\), \(i = 1 \dotso n\), we have

\[1 / L_{eff} = \sum_{i = 1}^n {1/{L_i}}\]

The program mne_inverse_operator calculates the decomposition \(A = \tilde{G} R^C = U \Lambda \bar{V^T}\), described in Computation of the solution. It is normally invoked from the convenience script mne_do_inverse_operator.

mne_make_movie is a program for producing movies and snapshot graphics frames without any graphics output to the screen. In addition, mne_make_movie can produce stc or w files which contain the numerical current estimate data in a simple binary format for postprocessing. These files can be displayed in mne_analyze, see Interactive analysis with mne_analyze, utilized in the cross-subject averaging process, see Morphing and averaging, and read into Matlab using the MNE Matlab toolbox, see Matlab toolbox.

The purpose of the utility mne_compute_raw_inverse is to compute inverse solutions from either evoked-response or raw data at specified ROIs (labels) and to save the results in a fif file which can be viewed with mne_browse_raw, read to Matlab directly using the MNE Matlab Toolbox, see Matlab toolbox, or converted to Matlab format using either mne_convert_mne_data, mne_raw2mat, or mne_epochs2mat. See mne_compute_raw_inverse for command-line options.

The fif files output from mne_compute_raw_inverse have various fields of the channel information set to facilitate interpretation by postprocessing software as follows:

**channel name**

Will be set to J[xyz] <number> , where the source component is indicated by the coordinat axis name and number is the vertex number, starting from zero, in the complete triangulation of the hemisphere in question.

**logical channel number**

Will be set to is the vertex number, starting from zero, in the complete triangulation of the hemisphere in question.

**sensor location**

The location of the vertex in head coordinates or in MRI coordinates, determined by the`--mricoord`

flag.

**sensor orientation**

Thex-direction unit vector will point to the direction of the current. Other unit vectors are set to zero. Again, the coordinate system in which the orientation is expressed depends on the`--mricoord`

flag.

The `--align_z`

flag tries to align the signs
of the signals at different vertices of the label. For this purpose,
the surface normals within the label are collected into a \(n_{vert} \times 3\) matrix.
The preferred orientation will be taken as the first right singular
vector of this matrix, corresponding to its largest singular value.
If the dot product of the surface normal of a vertex is negative,
the sign of the estimates at this vertex are inverted. The inversion
is reflected in the current direction vector listed in the channel
information, see above.

Note

The raw data files output by mne_compute_raw_inverse can be converted to mat files with mne_raw2mat. Alternatively, the files can be read directly from Matlab using the routines in the MNE Matlab toolbox, see Matlab toolbox. The evoked data output can be easily read directly from Matlab using the fiff_load_evoked routine in the MNE Matlab toolbox. Both raw data and evoked output files can be loaded into mne_browse_raw, see Browsing raw data with mne_browse_raw.