MNE-MATLAB toolbox

Overview

The MNE software contains a collection Matlab m-files to facilitate interfacing with binary file formats of the MNE software. The toolbox is located at $MNE_ROOT/share/matlab . The names of the MNE Matlab toolbox functions begin either with mne_ or with fiff_ . When you source the mne_setup script as described in Setting up MNE-C environment, one of the following actions takes place:

  • If you do not have the Matlab startup.m file, it will be created and lines allowing access to the MNE Matlab toolbox are added.
  • If you have startup.m and it does not have the standard MNE Matlab toolbox setup lines, you will be instructed to add them manually.
  • If you have startup.m and the standard MNE Matlab toolbox setup lines are there, nothing happens.

A summary of the available routines is provided in Tables High-level reading routines. - Examples demonstrating the use of the toolbox.. The toolbox also contains a set of examples which may be useful starting points for your own development. The names of these functions start with mne_ex and they are listed in Examples demonstrating the use of the toolbox..

Note

The MNE Matlab Toolbox is compatible with Matlab versions 7.0 or later.

Note

The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible initial skip in the file, i.e., the time between the start of the data acquisition and the start of saving the data to disk. The first_samp member of the returned structure indicates the initial skip in samples. If you want your own routines, which assume that initial skip has been removed, perform identically with the previous version, subtract first_samp from the sample numbers you specify to fiff_read_raw_segment . Furthermore, fiff_setup_read_raw has an optional argument to allow reading of unprocessed MaxShield data acquired with the Elekta MEG systems.

High-level reading routines.
Function Purpose
fiff_find_evoked Find all evoked data sets from a file.
fiff_read_bad_channels Read the bad channel list.
fiff_read_ctf_comp Read CTF software gradient compensation data.
fiff_read_evoked Read evoked-response data.
fiff_read_evoked_all Read all evoked-response data from a file.
fiff_read_meas_info Read measurement information.
fiff_read_mri Read an MRI description file.
fiff_read_proj Read signal-space projection data.
fiff_read_raw_segment Read a segment of raw data with time limits are specified in samples.
fiff_read_raw_segment_times Read a segment of raw data with time limits specified in seconds.
fiff_setup_read_raw Set up data structures before using fiff_read_raw_segment or fiff_read_raw_segment_times.
Channel selection utilities.
Function Purpose
fiff_pick_channels Create a selector to pick desired channels from data according to include and exclude lists.
fiff_pick_channels_evoked Pick desired channels from evoked-response data according to include and exclude lists.
fiff_pick_info Modify measurement info to include only selected channels.
fiff_pick_types Create a selector to pick desired channels from data according to channel types (MEG, EEG, STIM) in combination with include and exclude lists.
fiff_pick_types_evoked Pick desired channels from evoked-response data according to channel types (MEG, EEG, STIM) in combination with include and exclude lists.
Coordinate transformation utilities.
Function Purpose
fiff_invert_transform Invert a coordinate transformation structure.
fiff_reset_ch_pos Reset channel position transformation to the default values present in the file.
fiff_transform_eeg_chs Transform electrode positions to another coordinate frame.
fiff_transform_meg_chs Apply a coordinate transformation to the sensor location data to bring the integration points to another coordinate frame.
Basic reading routines.
Function Purpose
fiff_define_constants Define a structure which contains the constant relevant to fif files.
fiff_dir_tree_find Find nodes of a given type in a directory tree structure.
fiff_list_dir_tree List a directory tree structure.
fiff_make_dir_tree Create a directory tree structure.
fiff_open Open a fif file and create the directory tree structure.
fiff_read_named_matrix Read a named matrix from a fif file.
fiff_read_tag Read one tag from a fif file.
fiff_read_tag_info Read the info of one tag from a fif file.
fiff_split_name_list Split a colon-separated list of names into a cell array of strings.
Writing routines.
Function Purpose
fiff_end_block Write a FIFF_END_BLOCK tag.
fiff_end_file Write the standard closing.
fiff_start_block Write a FIFF_START_BLOCK tag.
fiff_start_file Write the appropriate beginning of a file.
fiff_write_ch_info Write a channel information structure.
fiff_write_coord_trans Write a coordinate transformation structure.
fiff_write_ctf_comp Write CTF compensation data.
fiff_write_dig_point Write one digitizer data point.
fiff_write_complex Write single-precision complex numbers.
fiff_write_complex_matrix Write a single-precision complex matrix.
fiff_write_double Write double-precision floats.
fiff_write_double_complex Write double-precision complex numbers.
fiff_write_double_complex_matrix Write a double-precision complex matrix.
fiff_write_double_matrix Write a double-precision matrix.
fiff_write_evoked Write an evoked-reponse data file.
fiff_write_float Write single-precision floats.
fiff_write_float_matrix Write a single-precision matrix.
fiff_write_id Write an id tag.
fiff_write_int Write 32-bit integers.
fiff_write_int_matrix Write a matrix of 32-bit integers.
fiff_write_name_list Write a name list.
fiff_write_named_matrix Write a named matrix.
fiff_write_proj Write SSP data.
fiff_write_short Write 16-bit integers.
fiff_write_string Write a string.
High-level data writing routines.
Function Purpose
fiff_write_evoked Write an evoked-response data file.
fiff_finish_writing_raw Write the closing tags to a raw data file.
fiff_start_writing_raw Start writing raw data file, i.e., write the measurement information.
fiff_write_dig_file Write a fif file containing digitization data.
fiff_write_raw_buffer Write one raw data buffer. This is used after a call to fiff_start_writing_raw.
Coil definition utilities.
Function Purpose
mne_add_coil_defs Add coil definitions to an array of channel information structures.
mne_load_coil_def Load a coil definition file.
Routines for software gradient compensation and signal-space projection.
Function Purpose
mne_compensate_to Apply or remove CTF software gradient compensation from evoked-response data.
mne_get_current_comp Get the state of software gradient compensation from measurement info.
mne_make_compensator Make a compensation matrix which switches the status of CTF software gradient compensation from one state to another.
mne_make_projector_info Create a signal-space projection operator with the projection item definitions and cell arrays of channel names and bad channel names as input.
mne_make_projector_info Like mne_make_projector but uses the measurement info structure as input.
mne_set_current_comp Change the information about the compensation status in measurement info.
High-level routines for reading MNE data files.
Function Purpose
mne_pick_channels_cov Pick desired channels from a sensor covariance matrix.
mne_pick_channels_forward Pick desired channels (rows) from a forward solution.
mne_read_bem_surfaces Read triangular tessellations of surfaces for boundary-element models.
mne_read_cov Read a covariance matrix.
mne_read_epoch Read an epoch of data from the output file of mne_epochs2mat.
mne_read_events Read an event list from a fif file produced by mne_browse_raw or mne_process_raw.
mne_read_forward_solution Read a forward solution from a fif file.
mne_read_inverse_operator Read an inverse operator from a fif file.
mne_read_morph_map Read an morphing map produced with mne_make_morph_maps, see Precomputing the morphing maps.
mne_read_noise_cov Read a noise-covariance matrix from a fif file.
mne_read_source_spaces Read source space information from a fif file.
High-level routines for writing MNE data files.
Function Purpose
mne_write_cov Write a covariance matrix to an open file.
mne_write_cov_file Write a complete file containing just a covariance matrix.
mne_write_events Write a fif format event file compatible with mne_browse_raw and mne_process_raw.
mne_write_inverse_sol_stc Write stc files containing an inverse solution or other dynamic data on the cortical surface.
mne_write_inverse_sol_w Write w files containing an inverse solution or other static data on the cortical surface.
Routines related to stc, w, and label files.
Function Purpose
mne_read_stc_file Read data from one stc file. The vertex numbering in the returned structure will start from 0.
mne_read_stc_file1 Read data from one stc file. The vertex numbering in the returned structure will start from 1.
mne_read_w_file Read data from one w file. The vertex numbering in the returned structure will start from 0.
mne_read_w_file1 Read data from one w file. The vertex numbering in the returned structure will start from 1.
mne_write_stc_file Write a new stc file. It is assumed the the vertex numbering in the input data structure containing the stc information starts from 0.
mne_write_stc_file1 Write a new stc file. It is assumed the the vertex numbering in the input data structure containing the stc information starts from 1.
mne_write_w_file Write a new w file. It is assumed the the vertex numbering in the input data structure containing the w file information starts from 0.
mne_write_w_file1 Write a new w file. It is assumed the the vertex numbering in the input data structure containing the w file information starts from 1.
mne_read_label_file Read a label file (ROI).
mne_write_label_file Write a label file (ROI).
mne_label_time_courses Extract time courses corresponding to a label from an stc file.
Routines for reading FreeSurfer surfaces.
Function Purpose
mne_read_curvature Read a curvature file.
mne_read_surface Read one surface, return the vertex locations and triangulation info.
mne_read_surfaces Read surfaces corresponding to one or both hemispheres. Optionally read curvature information and add derived surface data.
mne_reduce_surface Reduce the number of triangles on a surface using the reducepatch Matlab function.
mne_write_surface Write a FreeSurfer surface file.
Utility functions.
Function Purpose
mne_block_diag Create a sparse block-diagonal matrix out of a vector.
mne_combine_xyz Calculate the square sum of the three Cartesian components of several vectors listed in one row or column vector.
mne_file_name Compose a file name relative to $MNE_ROOT.
mne_find_channel Find a channel by name from measurement info.
mne_find_source_space_hemi Determine whether a given source space belongs to the left or right hemisphere.
mne_fread3 Read a three-byte integer.
mne_fwrite3 Write a three-byte integer.
mne_make_combined_event_file Combine data from several trigger channels into one event file.
mne_omit_first_line Omit first line from a multi-line message. This routine is useful for formatting error messages.
mne_prepare_inverse_operator Prepare inverse operator data for calculating L2 minimum-norm solutions and dSPM.
mne_setup_toolbox Set up the MNE Matlab toolbox.
mne_transform_coordinates Transform locations between different coordinate systems. This function uses the output file from mne_collect_transforms described in mne_collect_transforms as input.
mne_transpose_named_matrix Create a transpose of a named matrix.
mne_transform_source_space_to Transform source space data to another coordinate frame.
Examples demonstrating the use of the toolbox.
Function Purpose
mne_ex_average_epochs Example of averaging epoch data produced by mne_epochs2mat, see mne_epochs2mat.
mne_ex_cancel_noise Example of noise cancellation procedures.
mne_ex_compute_inverse Example of computing a L2 minimum-norm estimate or a dSPM solution.
mne_ex_data_sets Example of listing evoked-response data sets.
mne_ex_evoked_grad_amp Compute tangential gradient amplitudes from planar gradiometer data.
mne_ex_read_epochs Read epoch data from a raw data file.
mne_ex_read_evoked Example of reading evoked-response data.
mne_ex_read_raw Example of reading raw data.
mne_ex_read_write_raw Example of processing raw data (read and write).

Note

In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called processing history block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enhanced to include these data to the output file as appropriate. If you have older raw data files created in Matlab from input which has been processed Maxfilter, it is necessary to copy the processing history block from the original to modified raw data file using the mne_copy_processing_history utility. The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the processing history since revision 2.5 of the MNE software.

Some data structures

The MNE Matlab toolbox relies heavily on structures to organize the data. This section gives detailed information about fields in the essential data structures employed in the MNE Matlab toolbox. In the structure definitions, data types referring to other MNE Matlab toolbox structures are shown in italics. In addition, FIFF constants. lists the values of various FIFF constants defined by fiff_define_constants.m . The documented structures are:

tag

Contains one tag from the fif file, see The tag structure..

taginfo

Contains the information about one tag, see The taginfo structure..

directory

Contains the tag directory as a tree structure, see The directory structure..

id

A fif ID, see The id structure..

named matrix

Contains a matrix with names for rows and/or columns, see The named matrix structure.. A named matrix is used to store, e.g., SSP vectors and forward solutions.

trans

A 4 x 4 coordinate-transformation matrix operating on augmented column vectors. Indication of the coordinate frames to which this transformation relates is included, see The trans structure..

dig

A Polhemus digitizer data point, see The dig structure..

coildef

The coil definition structure useful for forward calculations and array visualization, see The coildef structure. For more detailed information, see BJEIAEIE.. For more detailed information on coil definitions, see Coil geometry information.

ch

Channel information structure, see The ch structure..

proj

Signal-space projection data, see The proj structure..

comp

Software gradiometer compensation data, see The comp structure..

measurement info

Translation of the FIFFB_MEAS_INFO entity, see The meas info structure.. This data structure is returned by fiff_read_meas_info .

surf

Used to represent triangulated surfaces and cortical source spaces, see The surf structure..

cov

Used for storing covariance matrices, see The cov structure..

fwd

Forward solution data returned by mne_read_forward_solution , see The fwd structure..

inv

Inverse operator decomposition data returned by mne_read_inverse_operator , see The inv structure. Note: The fields proj, whitener, reginv, and noisenorm are filled in by the routine mne_prepare_inverse_operator.. For more information on inverse operator decomposition, see Minimum-norm estimates. For an example on how to compute inverse solution using this data, see the sample routine mne_ex_compute_inverse .

Note

The MNE Matlab toolbox tries it best to employ vertex numbering starting from 1 as opposed to 0 as recorded in the data files. There are, however, two exceptions where explicit attention to the vertex numbering convention is needed. First, the standard stc and w file reading and writing routines return and assume zero-based vertex numbering. There are now versions with names ending with ‘1’, which return and assume one-based vertex numbering, see Routines related to stc, w, and label files.. Second, the logno field of the channel information in the data files produced by mne_compute_raw_inverse is the zero-based number of the vertex whose source space signal is contained on this channel.

FIFF constants.
Name Value Purpose
FIFFV_MEG_CH 1 This is a MEG channel.
FIFFV_REF_MEG_CH 301 This a reference MEG channel, located far away from the head.
FIFFV_EEF_CH 2 This is an EEG channel.
FIFFV_MCG_CH 201 This a MCG channel.
FIFFV_STIM_CH 3 This is a digital trigger channel.
FIFFV_EOG_CH 202 This is an EOG channel.
FIFFV_EMG_CH 302 This is an EMG channel.
FIFFV_ECG_CH 402 This is an ECG channel.
FIFFV_MISC_CH 502 This is a miscellaneous analog channel.
FIFFV_RESP_CH 602 This channel contains respiration monitor output.
FIFFV_COORD_UNKNOWN 0 Unknown coordinate frame.
FIFFV_COORD_DEVICE 1 The MEG device coordinate frame.
FIFFV_COORD_ISOTRAK 2 The Polhemus digitizer coordinate frame (does not appear in data files).
FIFFV_COORD_HPI 3 HPI coil coordinate frame (does not appear in data files).
FIFFV_COORD_HEAD 4 The MEG head coordinate frame (Neuromag convention).
FIFFV_COORD_MRI 5 The MRI coordinate frame.
FIFFV_COORD_MRI_SLICE 6 The coordinate frame of a single MRI slice.
FIFFV_COORD_MRI_DISPLAY 7 The preferred coordinate frame for displaying the MRIs (used by MRIlab).
FIFFV_COORD_DICOM_DEVICE 8 The DICOM coordinate frame (does not appear in files).
FIFFV_COORD_IMAGING_DEVICE 9 A generic imaging device coordinate frame (does not appear in files).
FIFFV_MNE_COORD_TUFTS_EEG 300 The Tufts EEG data coordinate frame.
FIFFV_MNE_COORD_CTF_DEVICE 1001 The CTF device coordinate frame (does not appear in files).
FIFFV_MNE_COORD_CTF_HEAD 1004 The CTF/4D head coordinate frame.
FIFFV_ASPECT_AVERAGE 100 Data aspect: average.
FIFFV_ASPECT_STD_ERR 101 Data aspect: standard error of mean.
FIFFV_ASPECT_SINGLE 102 Single epoch.
FIFFV_ASPECT_SUBAVERAGE 103 One subaverage.
FIFFV_ASPECT_ALTAVERAGE 104 One alternating (plus-minus) subaverage.
FIFFV_ASPECT_SAMPLE 105 A sample cut from raw data.
FIFFV_ASPECT_POWER_DENSITY 106 Power density spectrum.
FIFFV_ASPECT_DIPOLE_WAVE 200 The time course of an equivalent current dipole.
FIFFV_BEM_SURF_ID_UNKNOWN -1 Unknown BEM surface.
FIFFV_BEM_SURF_ID_BRAIN 1 The inner skull surface
FIFFV_BEM_SURF_ID_SKULL 3 The outer skull surface
FIFFV_BEM_SURF_ID_HEAD 4 The scalp surface
FIFFV_MNE_SURF_LEFT_HEMI 101 Left hemisphere cortical surface
FIFFV_MNE_SURF_RIGHT_HEMI 102 Right hemisphere cortical surface
FIFFV_POINT_CARDINAL 1 Digitization point which is a cardinal landmark aka. fiducial point
FIFFV_POINT_HPI 2 Digitized HPI coil location
FIFFV_POINT_EEG 3 Digitized EEG electrode location
FIFFV_POINT_ECG 3 Digitized ECG electrode location
FIFFV_POINT_EXTRA 4 Additional head surface point
FIFFV_POINT_LPA 1 Identifier for left auricular landmark
FIFFV_POINT_NASION 2 Identifier for nasion
FIFFV_POINT_RPA 3 Identifier for right auricular landmark
FIFFV_MNE_FIXED_ORI 1 Fixed orientation constraint used in the computation of a forward solution.
FIFFV_MNE_FREE_ORI 2 No orientation constraint used in the computation of a forward solution
FIFFV_MNE_MEG 1 Indicates an inverse operator based on MEG only
FIFFV_MNE_EEG 2 Indicates an inverse operator based on EEG only.
FIFFV_MNE_MEG_EEG 3 Indicates an inverse operator based on both MEG and EEG.
FIFFV_MNE_UNKNOWN_COV 0 An unknown covariance matrix
FIFFV_MNE_NOISE_COV 1 Indicates a noise covariance matrix.
FIFFV_MNE_SENSOR_COV 1 Synonym for FIFFV_MNE_NOISE_COV
FIFFV_MNE_SOURCE_COV 2 Indicates a source covariance matrix
FIFFV_MNE_FMRI_PRIOR_COV 3 Indicates a covariance matrix associated with fMRI priors
FIFFV_MNE_SIGNAL_COV 4 Indicates the data (signal + noise) covariance matrix
FIFFV_MNE_DEPTH_PRIOR_COV 5 Indicates the depth prior (depth weighting) covariance matrix
FIFFV_MNE_ORIENT_PRIOR_COV 6 Indicates the orientation (loose orientation constrain) prior covariance matrix
FIFFV_PROJ_ITEM_NONE 0 The nature of this projection item is unknown
FIFFV_PROJ_ITEM_FIELD 1 This is projection item is a generic field pattern or field patters.
FIFFV_PROJ_ITEM_DIP_FIX 2 This projection item is the field of one dipole
FIFFV_PROJ_ITEM_DIP_ROT 3 This projection item corresponds to the fields of three or two orthogonal dipoles at some location.
FIFFV_PROJ_ITEM_HOMOG_GRAD 4 This projection item contains the homogeneous gradient fields as seen by the sensor array.
FIFFV_PROJ_ITEM_HOMOG_FIELD 5 This projection item contains the three homogeneous field components as seen by the sensor array.
FIFFV_MNE_PROJ_ITEM_EEG_AVREF 10 This projection item corresponds to the average EEG reference.
The tag structure.
Field Data type Description
kind int32 The kind of the data item.
type uint32 The data type used to represent the data.
size int32 Size of the data in bytes.
next int32 Byte offset of the next tag in the file.
data various The data itself.
The taginfo structure.
Field Data type Description
kind double The kind of the data item.
type double The data type used to represent the data.
size double Size of the data in bytes.
pos double Byte offset to this tag in the file.
The directory structure.
Field Data type Description
block double The block id of this directory node.
id id The unique identifier of this node.
parent_id id The unique identifier of the node this node was derived from.
nent double Number of entries in this node.
nchild double Number of children to this node.
dir taginfo Information about tags in this node.
children directory The children of this node.
The id structure.
Field Data type Description
version int32 The fif file version (major < < 16 | minor).
machid int32(2) Unique identifier of the computer this id was created on.
secs int32 Time since January 1, 1970 (seconds).
usecs int32 Time since January 1, 1970 (microseconds past secs ).
The named matrix structure.
Field Data type Description
nrow int32 Number of rows.
ncol int32 Number of columns.
row_names cell(*) The names of associated with the rows. This member may be empty.
col_names cell(*) The names of associated with the columns. This member may be empty.
data various The matrix data, usually of type single or double.
The trans structure.
Field Data Type Description
from int32 The source coordinate frame, see FIFF constants.. Look for entries starting with FIFFV_COORD or FIFFV_MNE_COORD.
to int32 The destination coordinate frame.
trans double(4,4) The 4-by-4 coordinate transformation matrix. This operates from augmented position column vectors given in from coordinates to give results in to coordinates.
The dig structure.
Field Data Type Description
kind int32 The type of digitizing point. Possible values are listed in FIFF constants.. Look for entries starting with FIFF_POINT.
ident int32 Identifier for this point.
r single(3) The location of this point.
The coildef structure. For more detailed information, see Coil geometry information.
Field Data Type Description
class double The coil (or electrode) class.
id double The coil (or electrode) id.
accuracy double Representation accuracy.
num_points double Number of integration points.
size double Coil size.
baseline double Coil baseline.
description char(*) Coil description.
coildefs double (num_points,7) Each row contains the integration point weight, followed by location [m] and normal.
FV struct Contains the faces and vertices which can be used to draw the coil for visualization.
The ch structure.
Field Data Type Description
scanno int32 Scanning order number, starting from 1.
logno int32 Logical channel number, conventions in the usage of this number vary.
kind int32 The channel type (FIFFV_MEG_CH, FIFF_EEG_CH, etc., see FIFF constants. ).
range double The hardware-oriented part of the calibration factor. This should be only applied to the continuous raw data.
cal double The calibration factor to bring the channels to physical units.
loc double(12) The channel location. The first three numbers indicate the location [m], followed by the three unit vectors of the channel-specific coordinate frame. These data contain the values saved in the fif file and should not be changed. The values are specified in device coordinates for MEG and in head coordinates for EEG channels, respectively.
coil_trans double(4,4) Initially, transformation from the channel coordinates to device coordinates. This transformation is updated by calls to fiff_transform_meg_chs and fiff_transform_eeg_chs.
eeg_loc double(6) The location of the EEG electrode in coord_frame coordinates. The first three values contain the location of the electrode [m]. If six values are present, the remaining ones indicate the location of the reference electrode for this channel.
coord_frame int32 Initially, the coordinate frame is FIFFV_COORD_DEVICE for MEG channels and FIFFV_COORD_HEAD for EEG channels.
unit int32 Unit of measurement. Relevant values are: 201 = T/m, 112 = T, 107 = V, and 202 = Am.
unit_mul int32 The data are given in unit s multiplied by 10unit_mul. Presently, unit_mul is always zero.
ch_name char(*) Name of the channel.
coil_def coildef The coil definition structure. This is present only if mne_add_coil_defs has been successfully called.
The proj structure.
Field Data Type Description
kind int32 The type of the projection item. Possible values are listed in FIFF constants.. Look for entries starting with FIFFV_PROJ_ITEM or FIFFV_MNE_PROJ_ITEM.
active int32 Is this item active, i.e., applied or about to be applied to the data.
data named matrix The projection vectors. The column names indicate the names of the channels associated to the elements of the vectors.
The comp structure.
Field Data Type Description
ctfkind int32 The kind of the compensation as stored in file.
kind int32 ctfkind mapped into small integer numbers.
save_calibrated logical Were the compensation data saved in calibrated form. If this field is false, the matrix will be decalibrated using the fields row_cals and col_cals when the compensation data are saved by the toolbox.
row_cals double(*) Calibration factors applied to the rows of the compensation data matrix when the data were read.
col_cals double(*) Calibration factors applied to the columns of the compensation data matrix when the data were read.
data named matrix The compensation data matrix. The row_names list the names of the channels to which this compensation applies and the col_names the compensation channels. For more information, see Applying software gradient compensation.
The meas info structure.
Field Data Type Description
file_id id The fif ID of the measurement file.
meas_id id The ID assigned to this measurement by the acquisition system or during file conversion.
nchan int32 Number of channels.
sfreq double Sampling frequency.
highpass double Highpass corner frequency [Hz]. Zero indicates a DC recording.
lowpass double Lowpass corner frequency [Hz].
chs ch(nchan) An array of channel information structures.
ch_names cell(nchan) Cell array of channel names.
dev_head_t trans The device to head transformation.
ctf_head_t trans The transformation from 4D/CTF head coordinates to Neuromag head coordinates. This is only present in 4D/CTF data.
dev_ctf_t trans The transformation from device coordinates to 4D/CTF head coordinates. This is only present in 4D/CTF data.
dig dig(*) The Polhemus digitization data in head coordinates.
bads cell(*) Bad channel list.
projs proj(*) SSP operator data.
comps comp(*) Software gradient compensation data.
The surf structure.
Field Data Type Description
id int32 The surface ID.
sigma double The electrical conductivity of the compartment bounded by this surface. This field is present in BEM surfaces only.
np int32 Number of vertices on the surface.
ntri int32 Number of triangles on the surface.
coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
rr double (np,3) The vertex locations.
nn double (np,3) The vertex normals. If derived surface data was not requested, this is empty.
tris int32 (ntri,3) Vertex numbers of the triangles in counterclockwise order as seen from the outside.
nuse int32 Number of active vertices, i.e., vertices included in a decimated source space.
inuse int32(np) Which vertices are in use.
vertno int32(nuse) Indices of the vertices in use.
curv double(np) Curvature values at the vertices. If curvature information was not requested, this field is empty or absent.
tri_area double (ntri) The triangle areas in m2.If derived surface data was not requested, this field will be missing.
tri_cent double (ntri,3) The triangle centroids. If derived surface data was not requested, this field will be missing.
tri_nn double (ntri,3) The triangle normals. If derived surface data was not requested, this field will be missing.
nuse_tri int32 Number of triangles in use. This is present only if the surface corresponds to a source space created with the --ico option.
use_tris int32 (nuse_tri) The vertices of the triangles in use in the complete triangulation. This is present only if the surface corresponds to a source space created with the --ico option.
nearest int32(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the nearest active source space vertex.
nearest_dist double(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the distance to the nearest active source space vertex.
dist double (np,np) Distances between vertices on this surface given as a sparse matrix. A zero off-diagonal entry in this matrix indicates that the corresponding distance has not been calculated.
dist_limit double The value given to mne_add_patch_info with the --dist option, see Command line options. This value is presently always negative, indicating that only distances between active source space vertices, as indicated by the vertno field of this structure, have been calculated.
The cov structure.
Field Data Type Description
kind double What kind of a covariance matrix (1 = noise covariance, 2 = source covariance).
diag double Is this a diagonal matrix.
dim int32 Dimension of the covariance matrix.
names cell(*) Names of the channels associated with the entries (may be empty).
data double (dim,dim) The covariance matrix. This a double(dim) vector for a diagonal covariance matrix.
projs proj(*) The SSP vectors applied to these data.
bads cell(*) Bad channel names.
nfree int32 Number of data points used to compute this matrix.
eig double(dim) The eigenvalues of the covariance matrix. This field may be empty for a diagonal covariance matrix.
eigvec double (dim,dim) The eigenvectors of the covariance matrix.
The fwd structure.
Field Data Type Description
source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2).
coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
nsource int32 Total number of source space points.
nchan int32 Number of channels.
sol named matrix The forward solution matrix.
sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see Field derivatives. This field is present only if the forward solution was computed with the --grad option, see mne_forward_solution.
mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
src surf(:) The description of the source spaces.
source_rr double (nsource,3) The source locations.
source_nn double(:,3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations).
The inv structure. Note: The fields proj, whitener, reginv, and noisenorm are filled in by the routine mne_prepare_inverse_operator.
Field Data Type Description
methods int32 Has the solution been computed using MEG data (1), EEG data (2), or both (3).
source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2).
nsource int32 Total number of source space points.
nchan int32 Number of channels.
coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
source_nn double(:,3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations).
sing double (nchan) The singular values, i.e., the diagonal values of \(\Lambda\), see Computation of the solution.
eigen_leads double (:,nchan) The matrix \(V\), see Computation of the solution.
eigen_fields double (nchan, nchan) The matrix \(U^T\), see Computation of the solution.
noise_cov cov The noise covariance matrix \(C\).
source_cov cov The source covariance matrix \(R\).
src surf(:) The description of the source spaces.
mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
nave double The number of averages.
projs proj(:) The SSP vectors which were active when the decomposition was computed.
proj double (nchan) The projection operator computed using projs.
whitener   A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations).
reginv double (nchan) The diagonal matrix \(\Gamma\), see Computation of the solution.
noisenorm double(:) A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations).

On-line documentation for individual routines

Each of the routines listed in Tables High-level reading routines. - Examples demonstrating the use of the toolbox. has on-line documentation accessible by saying help <routine name> in Matlab.