MNE-CPP
beta 1.0
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Inverse operator. More...
#include <mne_inverse_operator.h>
Public Types | |
typedef QSharedPointer< MNEInverseOperator > | SPtr |
typedef QSharedPointer< const MNEInverseOperator > | ConstSPtr |
Public Member Functions | |
MNEInverseOperator () | |
MNEInverseOperator (QIODevice &p_IODevice) | |
MNEInverseOperator (const FiffInfo &info, MNEForwardSolution forward, const FiffCov &p_noise_cov, float loose=0.2f, float depth=0.8f, bool fixed=false, bool limit_depth_chs=true) | |
MNEInverseOperator (const MNEInverseOperator &p_MNEInverseOperator) | |
~MNEInverseOperator () | |
bool | assemble_kernel (const Label &label, QString method, bool pick_normal, MatrixXd &K, SparseMatrix< double > &noise_norm, QList< VectorXi > &vertno) |
bool | check_ch_names (const FiffInfo &info) const |
MatrixXd | cluster_kernel (const AnnotationSet &p_AnnotationSet, qint32 p_iClusterSize, MatrixXd &p_D, QString p_sMethod="cityblock") const |
MatrixXd & | getKernel () |
MatrixXd | getKernel () const |
bool | isFixedOrient () const |
MNEInverseOperator | prepare_inverse_operator (qint32 nave, float lambda2, bool dSPM, bool sLORETA=false) const |
void | write (QIODevice &p_IODevice) |
void | writeToStream (FiffStream *p_pStream) |
Static Public Member Functions | |
static MNEInverseOperator | make_inverse_operator (const FiffInfo &info, MNEForwardSolution forward, const FiffCov &p_noise_cov, float loose=0.2f, float depth=0.8f, bool fixed=false, bool limit_depth_chs=true) |
static bool | read_inverse_operator (QIODevice &p_IODevice, MNEInverseOperator &inv) |
Public Attributes | |
FiffInfoBase | info |
fiff_int_t | methods |
fiff_int_t | source_ori |
fiff_int_t | nsource |
fiff_int_t | nchan |
fiff_int_t | coord_frame |
MatrixXf | source_nn |
VectorXd | sing |
bool | eigen_leads_weighted |
FiffNamedMatrix::SDPtr | eigen_leads |
FiffNamedMatrix::SDPtr | eigen_fields |
FiffCov::SDPtr | noise_cov |
FiffCov::SDPtr | source_cov |
FiffCov::SDPtr | orient_prior |
FiffCov::SDPtr | depth_prior |
FiffCov::SDPtr | fmri_prior |
MNESourceSpace | src |
FiffCoordTrans | mri_head_t |
fiff_int_t | nave |
QList< FiffProj > | projs |
MatrixXd | proj |
MatrixXd | whitener |
VectorXd | reginv |
SparseMatrix< double > | noisenorm |
Friends | |
std::ostream & | operator<< (std::ostream &out, const MNELIB::MNEInverseOperator &p_MNEInverseOperator) |
typedef QSharedPointer<const MNEInverseOperator> MNELIB::MNEInverseOperator::ConstSPtr |
Const shared pointer type for MNEInverseOperator.
Definition at line 170 of file mne_inverse_operator.h.
typedef QSharedPointer<MNEInverseOperator> MNELIB::MNEInverseOperator::SPtr |
Shared pointer type for MNEInverseOperator.
Definition at line 169 of file mne_inverse_operator.h.
MNEInverseOperator::MNEInverseOperator | ( | ) |
Default constructor
Definition at line 61 of file mne_inverse_operator.cpp.
MNEInverseOperator::MNEInverseOperator | ( | QIODevice & | p_IODevice | ) |
Constructs an inverse operator, by reading from a IO device.
[in] | p_IODevice | IO device to read from the evoked data set. |
Definition at line 82 of file mne_inverse_operator.cpp.
MNEInverseOperator::MNEInverseOperator | ( | const FiffInfo & | info, |
MNEForwardSolution | forward, | ||
const FiffCov & | p_noise_cov, | ||
float | loose = 0.2f , |
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float | depth = 0.8f , |
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bool | fixed = false , |
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bool | limit_depth_chs = true |
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Constructs an inverse operator by making one.
[in] | info | The measurement info to specify the channels to include. Bad channels in info['bads'] are not used. |
[in] | forward | Forward operator. |
[in] | p_noise_cov | The noise covariance matrix. |
[in] | loose | float in [0, 1]. Value that weights the source variances of the dipole components defining the tangent space of the cortical surfaces. |
[in] | depth | float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed. |
[in] | fixed | Use fixed source orientations normal to the cortical mantle. If True, the loose parameter is ignored. |
[in] | limit_depth_chs | 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. |
Definition at line 90 of file mne_inverse_operator.cpp.
MNEInverseOperator::MNEInverseOperator | ( | const MNEInverseOperator & | p_MNEInverseOperator | ) |
Copy constructor.
[in] | p_MNEInverseOperator | MNE forward solution |
Definition at line 98 of file mne_inverse_operator.cpp.
MNEInverseOperator::~MNEInverseOperator | ( | ) |
Destroys the MNEInverseOperator.
Definition at line 130 of file mne_inverse_operator.cpp.
bool MNEInverseOperator::assemble_kernel | ( | const Label & | label, |
QString | method, | ||
bool | pick_normal, | ||
MatrixXd & | K, | ||
SparseMatrix< double > & | noise_norm, | ||
QList< VectorXi > & | vertno | ||
) |
Simple matrix multiplication followed by combination of the current components
This does all the data transformations to compute the weights for the eigenleads
[in] | label | labels. |
[in] | method | The applied normals. ("MNE" | "dSPM" | "sLORETA") |
[in] | pick_normal | Pick normals. |
[out] | K | Kernel. |
[out] | noise_norm | Noise normals. |
[out] | vertno | Vertices of the hemispheres. |
Definition at line 138 of file mne_inverse_operator.cpp.
bool MNEInverseOperator::check_ch_names | ( | const FiffInfo & | info | ) | const |
Check that channels in inverse operator are measurements.
[in] | info | The measurement info |
Definition at line 284 of file mne_inverse_operator.cpp.
MatrixXd MNEInverseOperator::cluster_kernel | ( | const AnnotationSet & | p_AnnotationSet, |
qint32 | p_iClusterSize, | ||
MatrixXd & | p_D, | ||
QString | p_sMethod = "cityblock" |
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) | const |
Clusters the current kernel
[in] | p_AnnotationSet | Annotation set containing the annotation of left & right hemisphere |
[in] | p_iClusterSize | Maximal cluster size per roi |
[out] | p_D | The cluster operator |
[in] | p_sMethod | "cityblock" or "sqeuclidean" |
Definition at line 330 of file mne_inverse_operator.cpp.
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Returns the current kernel
Definition at line 392 of file mne_inverse_operator.h.
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Returns the current kernel
Definition at line 400 of file mne_inverse_operator.h.
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inline |
Has inverse operator fixed orientation?
Definition at line 408 of file mne_inverse_operator.h.
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Assembles the inverse operator.
[in] | info | The measurement info to specify the channels to include. Bad channels in info['bads'] are not used. |
[in] | forward | Forward operator. |
[in] | p_noise_cov | The noise covariance matrix. |
[in] | loose | float in [0, 1]. Value that weights the source variances of the dipole components defining the tangent space of the cortical surfaces. |
[in] | depth | float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed. |
[in] | fixed | Use fixed source orientations normal to the cortical mantle. If True, the loose parameter is ignored. |
[in] | limit_depth_chs | 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. |
Definition at line 666 of file mne_inverse_operator.cpp.
MNEInverseOperator MNEInverseOperator::prepare_inverse_operator | ( | qint32 | nave, |
float | lambda2, | ||
bool | dSPM, | ||
bool | sLORETA = false |
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) | const |
mne_prepare_inverse_operator
Prepare for actually computing the inverse
[in] | nave | Number of averages (scales the noise covariance) |
[in] | lambda2 | The regularization factor |
[in] | dSPM | Compute the noise-normalization factors for dSPM? |
[in] | sLORETA | Compute the noise-normalization factors for sLORETA? |
Definition at line 905 of file mne_inverse_operator.cpp.
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static |
mne_read_inverse_operator
Reads the inverse operator decomposition from a fif file
[in] | p_IODevice | A fiff IO device like a fiff QFile or QTCPSocket |
[out] | inv | The read inverse operator |
Definition at line 1080 of file mne_inverse_operator.cpp.
void MNEInverseOperator::write | ( | QIODevice & | p_IODevice | ) |
write_inverse_operator
Writes an inverse operator to a fif file
[in] | p_IODevice | IO device to write the inverse operator to. |
Definition at line 1328 of file mne_inverse_operator.cpp.
void MNEInverseOperator::writeToStream | ( | FiffStream * | p_pStream | ) |
Writes the inverse operator to a FIFF stream
[in] | p_pStream | The stream to write to. |
Definition at line 1343 of file mne_inverse_operator.cpp.
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friend |
overloading the stream out operator<<
[in] | out | The stream to which the fiff covariance should be assigned to. |
[in] | p_MNEInverseOperator | MNEInverseOperator which should be assigned to the stream. |
Definition at line 416 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::coord_frame |
Coordinate system definition
Definition at line 363 of file mne_inverse_operator.h.
FiffCov::SDPtr MNELIB::MNEInverseOperator::depth_prior |
Depth priors
Definition at line 372 of file mne_inverse_operator.h.
FiffNamedMatrix::SDPtr MNELIB::MNEInverseOperator::eigen_fields |
Eigen fields
Definition at line 368 of file mne_inverse_operator.h.
FiffNamedMatrix::SDPtr MNELIB::MNEInverseOperator::eigen_leads |
Eigen leads
Definition at line 367 of file mne_inverse_operator.h.
bool MNELIB::MNEInverseOperator::eigen_leads_weighted |
If eigen lead are weighted.
Definition at line 366 of file mne_inverse_operator.h.
FiffCov::SDPtr MNELIB::MNEInverseOperator::fmri_prior |
fMRI priors
Definition at line 373 of file mne_inverse_operator.h.
FiffInfoBase MNELIB::MNEInverseOperator::info |
light weighted measurement info
Definition at line 358 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::methods |
MEG, EEG or both
Definition at line 359 of file mne_inverse_operator.h.
FiffCoordTrans MNELIB::MNEInverseOperator::mri_head_t |
MRI head coordinate transformation
Definition at line 375 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::nave |
Number of averages used to regularize the solution. Set to 1 on single Epoch by default.
Definition at line 376 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::nchan |
Number of channels.
Definition at line 362 of file mne_inverse_operator.h.
FiffCov::SDPtr MNELIB::MNEInverseOperator::noise_cov |
Noise covariance matrix.
Definition at line 369 of file mne_inverse_operator.h.
SparseMatrix<double> MNELIB::MNEInverseOperator::noisenorm |
These are the noise-normalization factors
Definition at line 381 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::nsource |
Number of source points.
Definition at line 361 of file mne_inverse_operator.h.
FiffCov::SDPtr MNELIB::MNEInverseOperator::orient_prior |
Orientation priors
Definition at line 371 of file mne_inverse_operator.h.
MatrixXd MNELIB::MNEInverseOperator::proj |
The projector to apply to the data.
Definition at line 378 of file mne_inverse_operator.h.
QList<FiffProj> MNELIB::MNEInverseOperator::projs |
SSP operator
Definition at line 377 of file mne_inverse_operator.h.
VectorXd MNELIB::MNEInverseOperator::reginv |
The diagonal matrix implementing. regularization and the inverse
Definition at line 380 of file mne_inverse_operator.h.
VectorXd MNELIB::MNEInverseOperator::sing |
Singular values
Definition at line 365 of file mne_inverse_operator.h.
FiffCov::SDPtr MNELIB::MNEInverseOperator::source_cov |
Source covariance matrix.
Definition at line 370 of file mne_inverse_operator.h.
MatrixXf MNELIB::MNEInverseOperator::source_nn |
Source normals.
Definition at line 364 of file mne_inverse_operator.h.
fiff_int_t MNELIB::MNEInverseOperator::source_ori |
Source orientation: f
Definition at line 360 of file mne_inverse_operator.h.
MNESourceSpace MNELIB::MNEInverseOperator::src |
Source Space
Definition at line 374 of file mne_inverse_operator.h.
MatrixXd MNELIB::MNEInverseOperator::whitener |
Whitens the data
Definition at line 379 of file mne_inverse_operator.h.