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MNEForwardSolution

Namespace: MNELIB  ·  Library: MNE Library

Python equivalent

mne.Forward in MNE-Python.

#include <mne/mne_forward_solution.h>

class MNELIB::MNEForwardSolution

Forward solution: leadfield matrix mapping source-space dipoles to sensor measurements, together with the source spaces, coordinate transforms and SSP/CTF state it was computed under.

In-memory representation of an -fwd.fif forward solution.

src/examples/ex_inv_api/main.cpp
FsLabel v1;
FsLabel::read(data + "/subjects/sample/label/lh.V1.label", v1);
QFile fwdFile(data + "/Result/ref-sample_audvis-meg-eeg-oct-6-fwd.fif");
const MNEForwardSolution fwd = MNEForwardSolution(fwdFile).pick_regions({v1}); // 70 sources x 3 orientations
QFile covFile(data + "/MEG/sample/sample_audvis-cov.fif");
const FiffCov noiseCov(covFile);
QFile aveFile(data + "/MEG/sample/sample_audvis-ave.fif");
const FiffEvoked evoked(aveFile, 0); // "Left Auditory"

const MNEInverseOperator inverse = MNEInverseOperator::make_inverse_operator(evoked.info, fwd, noiseCov, 0.2f, 0.8f);
const float lambda2 = 1.0f / 9.0f; // SNR 3
InvMinimumNorm dspm(inverse, lambda2, "dSPM");
const InvSourceEstimate stc = dspm.calculateInverse(evoked); // one row per source, combined over orientations

Public Methods​

MNEForwardSolution()​

Default constructor.

MNEForwardSolution(p_IODevice, force_fixed, surf_ori, include, exclude, bExcludeBads)​

Constructs a forward operator, by reading from a IO device.

Parameters:

  • p_IODevice : QIODevice & IO device to read from the forward operator.

  • force_fixed : bool Force fixed source orientation mode? (optional).

  • surf_ori : bool Use surface based source coordinate system? (optional).

  • include : const QStringList & Include these channels (optional).

  • exclude : const QStringList & Exclude these channels (optional).

  • bExcludeBads : bool Drop the channels marked bad in the file; mne.read_forward_solution keeps them.

MNEForwardSolution(p_MNEForwardSolution)​

Copy constructor.

Parameters:

  • p_MNEForwardSolution : const MNEForwardSolution & MNE forward solution.

operator=(other)​

Copy assignment operator.

Copies public data fields only (not computation state).

Parameters:

Returns:

MNEForwardSolution(other)​

Move constructs an MNEForwardSolution.

Parameters:

  • other : MNEForwardSolution && Forward solution to move from; left in a valid but unspecified state.

operator=(other)​

Move assignment operator.

Parameters:

  • other : MNEForwardSolution && Forward solution to move from; left in a valid but unspecified state.

Returns:

~MNEForwardSolution()​

Destroys the MNEForwardSolution.

clear()​

Initializes the MNE forward solution.

cluster_forward_solution(p_AnnotationSet, p_iClusterSize, p_D, p_pNoise_cov, p_pInfo, p_sMethod)​

Cluster the forward solution and stores the result to p_fwdOut.

The clustering is done by using the provided annotations

Parameters:

  • p_AnnotationSet : const FsAnnotationSet & FsAnnotation set containing the annotation of left & right hemisphere.

  • p_iClusterSize : qint32 Maximal cluster size per roi.

  • p_D : Eigen::MatrixXd & The cluster operator.

  • p_pNoise_cov : const FiffCov & Noise covariance used to whiten the gain matrix before clustering (optional).

  • p_pInfo : const FiffInfo & Measurement info matching the noise covariance (optional).

  • p_sMethod : QString "cityblock" or "sqeuclidean".

Returns:

compute_orient_prior(loose)​

Compute orientation prior.

Parameters:

  • loose : float The loose orientation parameter.

Returns:

isClustered()​

Indicates whether fwd conatins a clustered forward solution.

Returns:

  • bool — true if forward solution is clustered, false otherwise.

isEmpty()​

True if FIFF measurement file information is empty.

Returns:

  • bool — true if FIFF measurement file information is empty.

isFixedOrient()​

Has forward operator fixed orientation?

Returns:

  • bool — true if forward operator has fixed orientation, false otherwise.

pick_channels(include, exclude)​

mne.fiff.pick_channels_forward

Pick channels from forward operator

Parameters:

  • include : const QStringList & List of channels to include. (if None, include all available).

  • exclude : const QStringList & Channels to exclude (if None, do not exclude any).

Returns:

pick_regions(p_qListLabels)​

Reduces a forward solution to selected regions.

Parameters:

  • p_qListLabels : const QList< FsLabel > & ROIs.

Returns:

pick_types(meg, eeg, include, exclude)​

mne.fiff.pick_types_forward

Pick by channel type and names from a forward operator

Parameters:

  • meg : bool Include MEG channels.

  • eeg : bool Include EEG channels.

  • include : const QStringList & Additional channels to include (if empty, do not add any).

  • exclude : const QStringList & Channels to exclude (if empty, do not exclude any).

Returns:

prepare_forward(p_info, p_noise_cov, p_pca, p_outFwdInfo, gain, p_outNoiseCov, p_outWhitener, p_outNumNonZero)​

Prepare forward for assembling the inverse operator.

Parameters:

  • p_info : const FiffInfo & The measurement info to specify the channels to include. Bad channels in info['bads'] are not used.

  • p_noise_cov : const FiffCov & The noise covariance matrix.

  • p_pca : bool Calculate pca or not.

  • p_outFwdInfo : FiffInfo & Selected channel names.

  • gain : Eigen::MatrixXd & Gain matrix.

  • p_outNoiseCov : FiffCov & noise covariance matrix.

  • p_outWhitener : Eigen::MatrixXd & Whitener.

  • p_outNumNonZero : qint32 & the rank (non zeros).

tripletSelection(p_vecIdxSelection)​

write(p_IODevice)​

Write the forward solution to a FIFF file.

Formerly write_solution (SVN MNE).

Splits the combined MEG/EEG forward matrix back into separate blocks for FIFF storage, writes source spaces, coordinate transforms, and parent file provenance.

Parameters:

  • p_IODevice : QIODevice & The I/O device (e.g. QFile) to write to.

Returns:

  • bool — True if succeeded, false otherwise.

reduce_forward_solution(p_iNumDipoles, p_D)​

reduces the forward solution and stores the result to p_fwdOut.

Parameters:

  • p_iNumDipoles : qint32 Desired number of dipoles.

  • p_D : Eigen::MatrixXd & The reduction operator.

Returns:

to_fixed_ori()​

Helper to convert the forward solution to fixed ori from free.

convert_to_surf_ori()​

Rotates a free-orientation solution into local surface coordinates (two tangential components, then the normal), using average patch normals when the source spaces carry them.

Equivalent of mne.convert_forward_solution(fwd, surf_ori=True). Does nothing if already surface-oriented or fixed.

getSourcePositionsByLabel(lPickedLabels, tSurfSetInflated)​

Returns the positions of the specified sources based on their beloning labels.

Parameters:

  • lPickedLabels : const QList< FsLabel > & The stream to which the MNE forward solution should be assigned to.

  • tSurfSetInflated : const FsSurfaceSet & The surface used to pick the source from, based on their index specified bzy this forward solution.

Returns:

  • Eigen::MatrixX3f — the source position in 3D space.

Static Methods​

compute_depth_prior(Gain, gain_info, is_fixed_ori, exp, limit, patch_areas, limit_depth_chs)​

Compute weighting for depth prior.

ToDo move this to FiffCov

Parameters:

  • Gain : const Eigen::MatrixXd & gain matrix.

  • gain_info : const FiffInfo & The measurement info to specify the channels to include.

  • is_fixed_ori : bool Fixed orientation?.

  • exp : double float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed. (optional; default = 0.8).

  • limit : double (optional; default = 10.0).

  • patch_areas : const Eigen::MatrixXd & (optional) Cortical patch area of each source position (m²); the source gain is divided by it, as in mne.forward.compute_depth_prior.

  • limit_depth_chs : bool If True, use only grad channels in depth weighting (equivalent to MNE C code). If grad chanels aren't present, only mag channels will be used (if no mag, then eeg). If False, use all channels. (optional).

Returns:

read(p_IODevice, fwd, force_fixed, surf_ori, include, exclude, bExcludeBads)​

Parameters:

  • p_IODevice : QIODevice & A fiff IO device like a fiff QFile or QTCPSocket.

  • fwd : MNEForwardSolution & A forward solution from a fif file.

  • force_fixed : bool Force fixed source orientation mode? (optional).

  • surf_ori : bool Use surface based source coordinate system? (optional).

  • include : const QStringList & Include these channels (optional).

  • exclude : const QStringList & Exclude these channels (optional).

  • bExcludeBads : bool Drop the channels marked bad in the file; mne.read_forward_solution keeps them.

Returns:

  • bool — true if succeeded, false otherwise.

restrict_gain_matrix(G, info)​

Restrict gain matrix entries for optimal depth weighting.

Parameters:

  • G : Eigen::MatrixXd & Gain matrix to be restricted; result is stored in place.

  • info : const FiffInfo & Fiff information.

Example​

Used in examples​

ex_inv_api​

Inverse library: minimum-norm estimates, resolution matrices, label time courses, sparse solvers.

src/examples/ex_inv_api/main.cpp, line 112
FsLabel v1;
FsLabel::read(data + "/subjects/sample/label/lh.V1.label", v1);
QFile fwdFile(data + "/Result/ref-sample_audvis-meg-eeg-oct-6-fwd.fif");
const MNEForwardSolution fwd = MNEForwardSolution(fwdFile).pick_regions({v1}); // 70 sources x 3 orientations
QFile covFile(data + "/MEG/sample/sample_audvis-cov.fif");
const FiffCov noiseCov(covFile);
QFile aveFile(data + "/MEG/sample/sample_audvis-ave.fif");
const FiffEvoked evoked(aveFile, 0); // "Left Auditory"

ex_connectivity​

Example of using the MNE-CPP Connectivity library.

src/examples/ex_connectivity/main.cpp, line 186
MNEForwardSolution t_clusteredFwd;
MNEForwardSolution t_Fwd;

ex_connectivity_comparison​

Example to compare connectivity methods.

src/examples/ex_connectivity_comparison/main.cpp, line 183
MNEForwardSolution t_clusteredFwd;
MNEForwardSolution t_Fwd;

Also used in ex_fwd_api, ex_roi_clustered_inverse_pwl_rap_music, ex_clustered_inverse_mne_raw, ex_clustered_inverse_pwl_rap_music_raw, ex_clustered_inverse_rap_music_raw, ex_disp_3D, ex_histogram, ex_inverse_pwl_rap_music, ex_inverse_rap_music, ex_read_fwd, ex_st_clustered_inverse_pwl_rap_music, ex_compute_forward, ex_dsp_rt, ex_inv_beamformer, ex_inverse_mne_raw, ex_read_fwd_disp_3D.

Authors of this file​