MNEMATLAB documentation¶
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 Configuring MNEC, 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 MNEC 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.
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 evokedresponse data. 
fiff_read_evoked_all 
Read all evokedresponse data from a file. 
fiff_read_meas_info 
Read measurement information. 
fiff_read_mri 
Read an MRI description file. 
fiff_read_proj 
Read signalspace 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. 
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 evokedresponse 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 evokedresponse data according to channel types (MEG, EEG, STIM) in combination with include and exclude lists. 
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. 
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 colonseparated list of names into a cell array of strings. 
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 singleprecision complex numbers. 
fiff_write_complex_matrix 
Write a singleprecision complex matrix. 
fiff_write_double 
Write doubleprecision floats. 
fiff_write_double_complex 
Write doubleprecision complex numbers. 
fiff_write_double_complex_matrix 
Write a doubleprecision complex matrix. 
fiff_write_double_matrix 
Write a doubleprecision matrix. 
fiff_write_evoked 
Write an evokedreponse data file. 
fiff_write_float 
Write singleprecision floats. 
fiff_write_float_matrix 
Write a singleprecision matrix. 
fiff_write_id 
Write an id tag. 
fiff_write_int 
Write 32bit integers. 
fiff_write_int_matrix 
Write a matrix of 32bit 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 16bit integers. 
fiff_write_string 
Write a string. 
Function 
Purpose 

fiff_write_evoked 
Write an evokedresponse 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. 
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. 
Function 
Purpose 

mne_compensate_to 
Apply or remove CTF software gradient compensation from evokedresponse 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 signalspace 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. 
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 boundaryelement 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 noisecovariance matrix from a fif file. 
mne_read_source_spaces 
Read source space information from a fif file. 
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. 
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. 
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. 
Function 
Purpose 

mne_block_diag 
Create a sparse blockdiagonal 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 threebyte integer. 
mne_fwrite3 
Write a threebyte 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 multiline message. This routine is useful for formatting error messages. 
mne_prepare_inverse_operator 
Prepare inverse operator data for calculating L2 minimumnorm 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_transpose_named_matrix 
Create a transpose of a named matrix. 
mne_transform_source_space_to 
Transform source space data to another coordinate frame. 
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 minimumnorm estimate or a dSPM solution. 
mne_ex_data_sets 
Example of listing evokedresponse 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 evokedresponse 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 ElektaNeuromag Maxfilter (TM) software, the socalled 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 coordinatetransformation 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 coil_geometry_information.. For more detailed information on coil definitions, see Coil geometry information.
ch
Channel information structure, see The ch structure..
proj
Signalspace 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. For more information on inverse operator decomposition, see Minimumnorm 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 zerobased vertex numbering. There are now versions with names ending with ‘1’, which return and assume onebased 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 zerobased number of the vertex whose source space signal is contained on this channel.
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 (plusminus) 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_PROJ_ITEM_EEG_AVREF 
10 
This projection item corresponds to the average EEG reference. 
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. 
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. 
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. 
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 ). 
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. 
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 4by4 coordinate transformation matrix. This operates from augmented position column vectors given in from coordinates to give results in to coordinates. 
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. 
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. 
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 hardwareoriented 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 channelspecific 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. 
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. 
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. 
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. 
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

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

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 offdiagonal 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 
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. 
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 
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). 
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). 
Online documentation for individual routines¶
Each of the routines listed in Tables Highlevel reading routines.  Examples demonstrating the use of the toolbox. has online documentation accessible by saying help
<routine name> in Matlab.