

.. _ch_mne:

=====================
The current estimates
=====================

.. contents:: Contents
   :local:
   :depth: 2

Overview
########

This Chapter describes the computation of the minimum-norm
estimates. This is accomplished with two programs: *mne_inverse_operator* and *mne_make_movie*.
The chapter starts with a mathematical description of the method,
followed by description of the two software modules. The interactive
program for inspecting data and inverse solutions, mne_analyze ,
is covered in :ref:`ch_interactive_analysis`.

.. _CBBDJFBJ:

Minimum-norm estimates
######################

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 linear inverse operator
===========================

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 :math:`M \times N` matrix

.. math::    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, :math:`C` is the data noise-covariance matrix
and :math:`R'` is the source covariance matrix.
The dimensions of these matrices are :math:`N \times M`, :math:`N \times N`,
and :math:`M \times M`, respectively. The :math:`M \times 1` source-strength
vector is obtained by multiplying the :math:`N \times 1` data
vector by :math:`M`.

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

.. _CBBHAAJJ:

Regularization
==============

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

.. math::    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 :math:`\lambda^2`.
Small :math:`\lambda^2` corresponds to large current amplitudes
and complex estimate current patterns while a large :math:`\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

.. math::    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 :ref:`CHDDHAGE`) and those predicted
by the model while the second term is a weighted-norm of the current
estimate. It is seen that, with increasing :math:`\lambda^2`,
the source term receive more weight and larger discrepancy between
the measured and predicted data is tolerable.

.. _CHDDHAGE:

Whitening and scaling
=====================

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

.. math::    \tilde{M} = R \tilde{G}^T (\tilde{G} R \tilde{G}^T + I)^{-1}\ ,

where :math:`\tilde{G} = C^{-^1/_2}G` is the spatially
whitened gain matrix. The expected current values are :math:`\hat{j} = Mx(t)`,
where :math:`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 :math:`C = U_C \Lambda_C^2 U_C^T` as :math:`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, :math:`C_0`, is scaled
by the number of averages, :math:`L`, *i.e.*, :math:`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 :math:`R` is
such that :math:`\text{trace}(\tilde{G} R \tilde{G}^T) / \text{trace}(I) = 1`. With this choice we
can approximate :math:`\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/ :math:`\lambda^2` relationship    given above works nicely for the whitened forward solution. In the    un-whitened case scaling with the trace ratio :math:`\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.

.. _CBBHEGAB:

Regularization of the noise-covariance matrix
=============================================

Since finite amount of data is usually available to compute
an estimate of the noise-covariance matrix :math:`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 :ref:`CBBHAAJJ`,

- The estimated current values, and

- The noise-normalized estimates, see :ref:`CBBEAICH`.

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.

The MNE software accomplishes the regularization by replacing
a noise-covariance matrix estimate :math:`C` with

.. math::    C' = C + \sum_k {\varepsilon_k \bar{\sigma_k}^2 I^{(k)}}\ ,

where the index :math:`k` goes across
the different channel groups (MEG planar gradiometers, MEG axial
gradiometers and magnetometers, and EEG), :math:`\varepsilon_k` are
the corresponding regularization factors, :math:`\bar{\sigma_k}` are
the average variances across the channel groups, and :math:`I^{(k)}` are
diagonal matrices containing ones at the positions corresponding
to the channels contained in each channel group. The values :math:`\varepsilon_k` can
be adjusted with the regularization options ``--magreg`` , ``--gradreg`` ,
and ``--eegreg`` specified at the time of the inverse operator
decomposition, see :ref:`CBBDDBGF`. The convenience script mne_do_inverse_solution has
the ``--magreg`` and ``--gradreg`` combined to
a single option, ``--megreg`` , see :ref:`CIHCFJEI`.
Suggested range of values for :math:`\varepsilon_k` is :math:`0.05 \dotso 0.2`.

.. _CHDBEHBC:

Computation of the solution
===========================

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

.. math::    A = \tilde{G} R^{^1/_2} = U \Lambda V^T

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

With the above SVD it is easy to show that

.. math::    \tilde{M} = R^{^1/_2} V \Gamma U^T

where the elements of the diagonal matrix :math:`\Gamma` are

.. math::    \gamma_k = \frac{1}{\lambda_k} \frac{\lambda_k^2}{\lambda_k^2 + \lambda^2}\ .

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

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

where :math:`\bar{v_k} = R^C v_k`, :math:`v_k` being
the :math:`k` th column of :math:`V`. It is thus seen that the current estimate is
a weighted sum of the 'modified' eigenleads :math:`v_k`.

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

.. _CBBEAICH:

Noise normalization
===================

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

.. math::    M C M^T = \tilde{M} \tilde{M}^T\ .

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

.. math::    \tilde{M} \tilde{M}^T\ = \bar{V} \Gamma^2 \bar{V}^T\ .

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

.. _CHDCACDC:

Predicted data
==============

Under noiseless conditions the SNR is infinite and thus leads
to :math:`\lambda^2 = 0` and the minimum-norm estimate
explains the measured data perfectly. Under realistic conditions,
however, :math:`\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 :math:`x(t)`,
and measured one can give valuable insight on the correctness of
the regularization applied.

In the SVD approach we easily find

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

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

.. _CBBDBHDI:

Cortical patch statistics
=========================

If the ``--cps`` option was used in source space
creation (see :ref:`CIHCHDAE`) or if mne_add_patch_info described
in :ref:`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 :math:`d`:

- The average over the normals of at the
  vertices in a patch, :math:`\bar{n_d}`,

- The areas of the patches, :math:`A_d`,
  and

- The average deviation of the vertex normals in a patch from
  their average, :math:`\sigma_d`, given in degrees.

The orientation constraints
===========================

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, :math:`\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 :math:`\sigma_d`, defined above.

.. _CBBDFJIE:

Depth weighting
===============

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

.. math::    f_p = (g_{1p}^T g_{1p} + g_{2p}^T g_{2p} + g_{3p}^T g_{3p})^{-\gamma}\ ,

where :math:`g_{1p}`, :math:`g_{2p}`, and :math:`g_{3p}` are the three columns
of :math:`G` corresponding to source location :math:`p` and :math:`\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.

.. _CBBDIJHI:

fMRI-guided estimates
=====================

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 :math:`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.

.. _CBBDGIAE:

Effective number of averages
############################

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

.. math::    C = C_0 / L_{eff}

where :math:`L_{eff}` is the effective
number of averages. To calculate :math:`L_{eff}` for
an arbitrary linear combination of conditions

.. math::    y(t) = \sum_{i = 1}^n {w_i x_i(t)}

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

.. math::    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

.. math::    1 / L_{eff} = \sum_{i = 1}^n {w_i^2 / L_i}

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

.. math::    w_i = L_i / \sum_{i = 1}^n {L_i}

and, therefore

.. math::    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 :math:`w_1 = 1` and :math:`w_2 = -1` and
thus

.. math::    1 / L_{eff} = 1 / L_1 + 1 / L_2

or

.. math::    L_{eff} = \frac{L_1 L_2}{L_1 + L_2}

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

.. math::    1 / L_{eff} = \sum_{i = 1}^n {1/{L_i}}

.. _CBBDDBGF:

Inverse-operator decomposition
##############################

The program :ref:`mne_inverse_operator` calculates
the decomposition :math:`A = \tilde{G} R^C = U \Lambda \bar{V^T}`,
described in :ref:`CHDBEHBC`. It is normally invoked from the convenience
script :ref:`mne_do_inverse_operator`. 


.. _CBBECEDE:

Producing movies and snapshots
##############################

:ref:`mne_make_movie` is a program
for producing movies and snapshot graphics frames without any graphics
output to the screen. In addition, :ref:`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 :ref:`mne_analyze`,
see :ref:`ch_interactive_analysis`, utilized in the cross-subject averaging
process, see :ref:`ch_morph`, and read into Matlab using the MNE
Matlab toolbox, see :ref:`ch_matlab`.


.. _CBBCGHAH:

Computing inverse from raw and evoked data
##########################################

The purpose of the utility :ref:`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 :ref:`mne_browse_raw`,
read to Matlab directly using the MNE Matlab Toolbox, see :ref:`ch_matlab`,
or converted to Matlab format using either :ref:`mne_convert_mne_data`,
:ref:`mne_raw2mat`, or :ref:`mne_epochs2mat`. See
:ref:`mne_compute_raw_inverse` for command-line options.

.. _CBBHJDAI:

Implementation details
======================

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**

    The *x*-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 :math:`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 :ref:`mne_compute_raw_inverse` can be converted to mat files with :ref:`mne_raw2mat`. Alternatively, the files can be read directly from Matlab using the routines in the MNE Matlab toolbox, see :ref:`ch_matlab`. 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 :ref:`mne_browse_raw`, see :ref:`ch_browse`.
