MNE-MATLAB documentation

This is a collection of MATLAB files to process MEG and EEG data. These files allow a nice interaction with the other MNE projects, including:

• MNE-C
• MNE-Python

This code is licensed under the BSD 3-clause. See LICENSE.txt

Original and principal contribution is from:

Matti Hamalainen
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown, MA, USA

Note

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

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 :ref:`user_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 the `MNE-C manual`_. 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.

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.
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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

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.
mne_transpose_named_matrix	Create a transpose of a named matrix.
mne_transform_source_space_to	Transform source space data to another coordinate frame.

.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}|

Examples demonstrating the use of the toolbox.

Function	Purpose
mne_ex_average_epochs	Example of averaging epoch data produced by 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, :ref:`matlab_fif_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 :ref:`BGBGIIGD`.

taginfo

Contains the information about one tag, see :ref:`BGBBJBJJ`.

directory

Contains the tag directory as a tree structure, see :ref:`BGBEDHBG`.

id

A fif ID, see :ref:`BGBDAHHJ`.

named matrix

Contains a matrix with names for rows and/or columns, see :ref:`BGBBEDID`. 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 :ref:`BGBDHBIF`.

dig

A Polhemus digitizer data point, see :ref:`BGBHDEDG`.

coildef

The coil definition structure useful for forward calculations and array visualization, see :ref:`BGBGBEBH`. For more detailed information on coil definitions, see :ref:`coil_geometry_information`.

ch

Channel information structure, see :ref:`BGBIABGD`.

proj

Signal-space projection data, see :ref:`BGBCJHJB`.

comp

Software gradiometer compensation data, see :ref:`BGBJDIFD`.

measurement info

Translation of the FIFFB_MEAS_INFO entity, see :ref:`BGBFHDIJ` and :class:`mne.Info`. This data structure is returned by fiff_read_meas_info, will not be as complete as :class:`mne.Info`.

surf

Used to represent triangulated surfaces and cortical source spaces, see :ref:`BGBEFJCB`.

cov

Used for storing covariance matrices, see :ref:`BGBJJIED`.

fwd

Forward solution data returned by mne_read_forward_solution , see :ref:`BGBFJIBJ`.

inv

Inverse operator decomposition data returned by mne_read_inverse_operator. For more information on inverse operator decomposition, see :ref:`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 :ref:`BABBDDAI`. 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.

.. tabularcolumns:: |p{0.38\linewidth}|p{0.06\linewidth}|p{0.46\linewidth}|

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 a.k.a. 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 patterns.
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_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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

The trans structure.

Field	Data Type	Description
from	int32	The source coordinate frame, see :ref:`matlab_fif_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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

The dig structure.

Field	Data Type	Description
kind	int32	The type of digitizing point. Possible values are listed in :ref:`matlab_fif_constants`. Look for entries starting with FIFF_POINT.
ident	int32	Identifier for this point.
r	single(3)	The location of this point.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

The coildef structure. For more detailed information, see :ref:`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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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 :ref:`matlab_fif_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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

The proj structure.

Field	Data Type	Description
kind	int32	The type of the projection item. Possible values are listed in :ref:`matlab_fif_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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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. 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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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.

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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. This field is present only if the forward solution was computed with the --grad option in MNE-C.
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).

.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|

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 :ref:`mne_solution`.
eigen_leads	double (:,nchan)	The matrix V, see :ref:`mne_solution`.
eigen_fields	double (nchan, nchan)	The matrix U^\top, see :ref:`mne_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 :ref:`mne_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 :ref:`BGBCGHAG` - :ref:`BGBEFADJ` has on-line documentation accessible by saying help <routine name> in Matlab.

Development

Tests can be run locally with:

$ matlab -nosplash -nodesktop -r "cd matlab; exit(~moxunit_runtests('test'))"

Or:

$ octave --no-gui --eval "cd matlab; exit(~moxunit_runtests('test'))"

Currently only epochs and raw are tested as the other test files require the sample dataset.