Browsing raw data with mne_browse_raw¶

Open¶

Selecting Open from file menu pops up the dialog shown in The Open dialog..

The Raw files and Maxfilter output buttons change the file name filter to include names which end with _raw.fif or sss.fif , respectively, to facilitate selection of original raw files or those processed with the Neuromag Maxfilter (TM) software

The options under Software gradient compensation allow selection of the compensation grade for the data. These selections apply to the CTF data only. The standard choices are No compensation and Third-order gradient. If other than No compensation is attempted for non-CTF data, an error will be issued. The compensation selection affects the averages and noise-covariance matrices subsequently computed. The desired compensation takes effect independent of the compensation state of the data in the file, i.e., already compensated data can be uncompensated and vice versa. For more information on software gradient compensation please consult Applying software gradient compensation.

The Keep the initial skip button controls how the initial segment of data not stored in the raw data file is handled. During the MEG acquisition data are collected continuously but saving to the raw data file is controlled by the Record raw button. Initial skip refers to the segment of data between the start of the recording and the first activation of Record raw . If Keep initial skip is set, this empty segment is taken into account in timing, otherwise time zero is set to the beginning of the data stored to disk.

When a raw data file is opened, the digital trigger channel is scanned for events. For large files this may take a while.

The Open dialog.

Open evoked¶

This menu item brings up a standard file selection dialog to load evoked-response data from files. All data sets from a file are loaded automatically and display in the average view window, see Topographical data displays. The data loaded are affected by the scale settings, see, Scales, the filter, see Filter, and the options selected in the Manage averages dialog, see Managing averages.

Save¶

It is possible to save filtered and projected data into a new raw data file. When you invoke the save option from the file menu, you will be prompted for the output file name and a down-sampling factor. The sampling frequency after down-sampling must be at least three times the lowpass filter corner frequency. The output will be split into files which are just below 2 GB so that the fif file maximum size is not exceed.

If <filename> ends with .fif or _raw.fif , these endings are deleted. After these modifications, _raw.fif is inserted after the remaining part of the file name. If the file is split into multiple parts, the additional parts will be called <name> - <number> _raw.fif . For downsampling and saving options in mne_process_raw , see mne_process_raw.

Change working directory¶

Brings up a file selection dialog which allows changing of the working directory.

Read projection¶

Selecting Read projection… from the File menu, pops up a dialog to enter a name of a file containing a signal-space projection operator to be applied to the data. There is an option to keep existing projection items.

Save projection¶

The Save projection… item in the File menu pops up a dialog to save the present projection operator into a file. Normally, the EEG average reference projection is not included. If you want to include it, mark the Include EEG average reference option. If your MEG projection includes items for both magnetometers and gradiometers and you want to use the projection operator file output from here in the Neuromag Signal processor (graph) software, mark the Enforce compatibility with graph option.

Apply bad channels¶

Applies the current selection of bad channels to the currently open raw file.

Load events (text)¶

Reads a text format event file. For more information on events, see Events and annotations.

Load events (fif)¶

Reads a fif format event file. For more information on events, see Events and annotations.

Save events (text)¶

Brings up a a dialog to save all or selected types of events into a text file. This file can be edited and used in the averaging and covariance matrix estimation as an input file to specify the time points of events, see Event files. For more information on events, see Events and annotations.

Save events (fif)¶

Save the events in fif format. These binary event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox, see Matlab toolbox. For more information on events, see Events and annotations.

Load derivations¶

This menu choice allows loading of channel derivation data files created with the mne_make_derivations utility, see mne_make_derivations, or using the interactive derivations editor in mne_browse_raw , see Derivations, Most common use of derivations is to calculate differences between EEG channels, i.e., bipolar EEG data. Since any number of channels can be included in a derivation with arbitrary weights, other applications are possible as well. Before a derivation is accepted to use, the following criteria have to be met:

• All channels to be combined into a single derivation must have identical units of measure.
• All channels in a single derivation have to be of the same kind, e.g., MEG channels or EEG channels.
• All channels specified in a derivation have to be present in the currently loaded data set.

Multiple derivation data files can be loaded by specifying the Keep previous derivations option in the dialog that specifies the derivation file to be loaded. After a derivation file has been successfully loaded, a list of available derivations will be shown in a message dialog.

Each of the derived channels has a name specified when the derivation file was created. The derived channels can be included in channel selections, see Selection. At present, derived channels cannot be displayed in topographical data displays. Derived channels are not included in averages or noise covariance matrix estimation.

Save derivations¶

Saves the current derivations into a file.

Load channel selections¶

This choice loads a new set of channel selections. The default directory for the selections is $HOME/.mne. If this directory does not exist, it will be created before bringing up the file selection dialog to load the selections.

Save channel selections¶

This choice brings up a dialog to save the current channel selections. This is particularly useful if the standard set of selections has been modified as explained in Selection. The default directory for the selections is $HOME/.mne. If this directory does not exist, it will be created before bringing up the file selection dialog to save the selections. Note that all currently existing selections will be saved, not just those added to the ones initially loaded.

Quit¶

Exits the program without questions asked.

Filter¶

Selecting Filter… from the Adjust menu pops up the dialog shown in The filter adjustment dialog..

The filter adjustment dialog.

The items in the dialog have the following functions:

Highpass (Hz)

The half-amplitude point of the highpass filter. The width of the transition from zero to one can be specified with the --highpassw command-line option, see mne_browse_raw. Lowest feasible highpass value is constrained by the length of the filter and sampling frequency. You will be informed when you press OK or Apply if the selected highpass could not be realized. The default value zero means no highpass filter is applied in addition to the analog highpass present in the data.

Lowpass (Hz)

The half-amplitude point of the lowpass filter.

Lowpass transition (Hz)

The width of the \(\cos^2\)-shaped transition from one to zero, centered at the Lowpass value.

Filter active

Selects whether or not the filter is applied to the data.

The filter is realized in the frequency domain and has a zero phase shift. When a filter is in effect, the value of the first sample in the file is subtracted from the data to correct for an initial dc offset. This procedure also eliminates any filter artifacts in the beginning of the data.

Scales¶

Selecting Scales… from the Adjust menu pops up the dialog shown in The Scales dialog..

The Scales dialog.

The items in the dialog have the following functions:

MEG (fT/cm)

Sets the scale for MEG planar gradiometer channels in fT/cm. All scale values are defined from zero to maximum, i.e., the viewport where signals are plotted in have the limits ± <scale value> .

MEG axmult (cm)

The scale for MEG magnetometers and axial gradiometers is defined by multiplying the gradiometer scale by this number, yielding units of fT.

EEG (\(\mu V\))

The scale for EEG channels in \(\mu V\).

EOG (\(\mu V\))

The scale for EOG channels in \(\mu V\).

ECG (mV)

The scale for ECG channels in mV.

EMG (mV)

The scale for EMG channels in mV.

MISC (V)

The scale for MISC channels in V.

Time span (s)

The length of raw data displayed in the main window at a time.

Show stimulus markers

Draw vertical lines at time points where the digital trigger channel has a transition from zero to a nonzero value.

Segment min. time (s)

It is possible to show data segments in the topographical (full view) layout, see below. This parameter sets the starting time point, relative to the selected time, to be displayed.

Segment max. time (s)

This parameter sets the ending time point, relative to the current time, to be displayed in the topographical layout.

Show segments in full view

Switches on the display of data segments in the topographical layout.

Show segments in sample view

Switches on the display of data segments in a “sidebar” to the right of the main display.

Show channel names

Show the names of the channels in the topographical displays.

Text size

Size of the channel number text as a fraction of the height of each viewport.

Show viewport frames

Show the boundaries of the viewports in the topographical displays.

Show zeroline and zerolevel

Show the zero level, i.e., the baseline level in the topographical displays. In addition, the zero time point is indicated in the average views if it falls to the time range, i.e., if the minimum of the time scale is negative and the maximum is positive.

Scale magnification for averages

For average displays, the scales are made more sensitive by this factor.

Average display baseline min (ms)

Sets the lower time limit for the average display baseline. This setting does not affect the averages stored.

Average display baseline max (ms)

Sets the upper time limit for the average display baseline. This setting does not affect the averages stored.

Use average display baseline

Switches the application of a baseline to the displayed averages on and off.

Average time range min (ms)

Sets the minimum time for the average display. This setting is inactive if Autoscale time range is on.

Average time range max (ms)

Sets the maximum time for the average data display. This setting is inactive if Autoscale time range is on.

Autoscale time range

Set the average display time range automatically to be long enough to accommodate all data.

Colors¶

Shows a dialog which allows changes to the default colors of various display items.

Derivations¶

Brings up the interactive derivations editor. This editor can be used to add or modify derived channels, i.e., linear combinations of signals actually recorded. Channel derivations can be also created and modified using the mne_make_derivations tool, see mne_make_derivations. The interactive editor contains two main areas:

• Interactive tools for specifying a channel linear combination. This tool is limited to combining up to five channels in each of the derivations. Clicking Add after defining the name of the new derivation, the weights of the component channels and their names, adds the corresponding arithmetic expression to the text area.
• Text area which contains the currently defined derivations as arithmetic expressions in a format identical to that used by mne_make_derivations . These expressions can be manually edited before accepting the new set of derivations. Initially, the text area will contain the derivations already defined.

The Define button interprets the arithmetic expressions in the text area as new derivations and closes the dialog. The Cancel button closes the dialog without any change in the derivations.

Recommended workflow for defining derived EEG channels and associated selections interactively involves the following steps:

• If desired, EEG channels can be relabeled with descriptive names using the mne_rename_channels utility, see mne_rename_channels. It is strongly recommended that you keep a copy of the channel alias file used by mne_rename_channels . If necessary, you can then easily return to the original channel names by running mne_rename_channels again with the --revert option.
• Load the data file into mne_browse_raw and use the interactive derivations editor to create the desired derived channels. These are usually differences between the signals in two EEG electrodes.
• Save the derivations from the file menu.
• If desired, move the derivations file to the standard location ($HOME/.mne/mne_browse_raw-deriv.fif ).
• Create new channel selections employing the original and derived channels using the channel selection tool described in Selection.
• Save the new channel selections from the file menu.
• If desired, change the order of the channels in the selections in the selection file by editing it in a text editor and move it to the standard location $HOME/.mne/mne_browse_raw.sel .

Selection¶

Brings up a dialog to select channels to be shown in the main raw data display. This dialog also allows modification of the set of channel selections as described below.

By default, the available selections are defined by the file $MNE_ROOT/share/mne/mne_browse_raw/mne_browse_raw.sel . This default channel selection file can be modified by copying the file into $HOME/.mne/mne_browse_raw.sel . The format of this text file should be self explanatory.

The channel selection dialog.

The channel selection dialog is shown in The channel selection dialog.. The number of items in the selection list depends on the contents of your selection file. If the list has the keyboard focus you can easily move from one selection to another with the up and down arrow keys.

The two buttons below the channel selection buttons facilitate the modification of the selections:

Add…

Brings up the selection dialog shown in Dialog to create a new channel selection. to create new channel selections.

Omit current

Delete the current channel selection. Deletion only affects the selections in the memory of the program. To save the changes permanently into a file, use Save channel selections… in the File menu, see Save channel selections.

Dialog to create a new channel selection.

The components of the selection creation dialog shown in Dialog to create a new channel selection. have the following functions:

List of channel names

The channels selected from this list will be included in the new channel selection. A selection can be extended with the control key. A range of channels can be selected with the shift key. The list contains both the original channels actually present in the file and the names of the channels in currently loaded derivation data, see Load derivations.

Regexp:

This provides another way to select channels. By entering here a regular expression as defined in IEEE Standard 1003.2 (POSIX.2), all channels matching it will be selected and added to the present selection. An empty expression deselects all items in the channel list. Some useful regular expressions are listed in Examples of regular expressions for channel selections. In the present version, regular matching does not look at the derived channels.

Name:

This text field specifies the name of the new selection.

Select

Select the channels specified by the regular expression. The same effect can be achieved by entering return in the Regexp: .

Add

Add a new channel selection which contains the channels selected from the channel name list. The name of the selection is specified with the Name: text field.

Full view layout¶

Shows a selection of available layouts for the topographical views (full view and average display). The system-wide layout files reside in $MNE_ROOT/share/mne/mne_analyze/lout . In addition any layout files residing in $HOME/.mne/lout are listed. The default layout is Vectorview-grad. If there is a layout file in the user’s private layout directory ending with -default.lout , that layout will be used as the default instead. The Default button returns to the default layout.

The format of the layout files is:

<plot area limits>

<viewport definition #1>

…

<viewport definition #N>

The <plot area limits> define the size of the plot area (\(x_{min}\ x_{max}\ y_{min}\ y_{max}\)) which should accommodate all view ports. When the layout is used, the plot area will preserve its aspect ratio; if the plot window has a different aspect ratio, there will be empty space on the sides.

The viewports define the locations of the individual channels in the plot. Each viewport definition consists of

<number> \(x_0\ y_0\) <width> <height> <name> [: <name> ] …

where number is a viewport number (not used by the MNE software), \(x_0\) and \(y_0\) are the coordinates of the lower-left corner of the viewport, <width> and <height> are the viewport dimensions, and <name> is a name of a channel. Multiple channel names can be specified by separating them with a colon.

When a measurement channel name is matched to a layout channel name, all spaces are removed from the channel names and the both the layout channel name and the data channel name are converted to lower case. In addition anything including and after a hyphen (-) is omitted. The latter convention facilitates using CTF MEG system data, which has the serial number of the system appended to the channel name with a dash. Removal of the spaces is important for the Neuromag Vectorview data because newer systems do not have spaces in the channel names like the original Vectorview systems did.

Projection¶

Lists the currently available signal-space projection (SSP) vectors and allows the activation and deactivation of items. For more information on SSP, see The Signal-Space Projection (SSP) method.

Compensation¶

Brings up a dialog to select software gradient compensation. This overrides the choice made at the open time. For details, see Open, above.

Averaging preferences¶

Averaging preferences.

Selecting Averaging preferences… from the Adjust menu pops up the dialog shown in Averaging preferences.. These settings apply only to the simple averages calculated with help of tools residing just below the main raw data display, see The tool bar. These settings are also applied when a covariance matrix is computed to create a SSP operator as described in Creating a new SSP operator and in the computation of a covariance matrix from raw data, see Estimation of a covariance matrix from raw data.

The items in the dialog have the following functions:

Starting time (ms)

Beginning time of the epoch to be averaged (relative to the trigger).

Ending time (ms)

Ending time of the epoch to be averaged.

Ignore around stimulus (ms)

Ignore this many milliseconds on both sides of the trigger when considering the epoch. This parameter is useful for ignoring large stimulus artefacts, e.g., from electrical somatosensory stimulation.

MEG grad rejection (fT/cm)

Rejection criterion for MEG planar gradiometers. If the peak-to-peak value of any planar gradiometer epoch exceed this value, it will be omitted. A negative value turns off rejection for a particular channel type.

MEG mag rejection (fT)

Rejection criterion for MEG magnetometers and axial gradiometers.

EEG rejection (\(\mu V\))

Rejection criterion for EEG channels.

EOG rejection (\(\mu V\))

Rejection criterion for EOG channels.

ECG rejection (mV)

Rejection criterion for ECG channels.

MEG grad no signal (fT/cm)

Signal detection criterion for MEG planar gradiometers. The peak-to-peak value of all planar gradiometer signals must exceed this value, for the epoch to be included. This criterion allows rejection of data with saturated or otherwise dysfunctional channels.

MEG mag no signal (fT)

Signal detection criterion for MEG magnetometers and axial gradiometers.

EEG no signal (\(\mu V\))

Signal detection criterion for EEG channels.

EOG no signal (\(\mu V\))

Signal detection criterion for EOG channels.

ECG no signal (mV)

Signal detection criterion for ECG channels.

Fix trigger skew

This option has the same effect as the FixSkew parameter in averaging description files, see Common parameters.

Trace color

The color assigned for the averaged traces in the display can be adjusted by pressing this button.

Averaging¶

The Average… menu item pops up a file selection dialog to access a description file for batch-mode averaging. The structure of these files is described in Description files for off-line averaging. All parameters for the averaging are taken from the description file, i.e., the parameters set in the averaging preferences dialog (Averaging preferences) do not effect the result.

Estimation of a covariance matrix¶

The Compute covariance… menu item pops up a file selection dialog to access a description file which specifies the options for the estimation of a covariance matrix. The structure of these files is described in Description files for covariance matrix estimation.

Estimation of a covariance matrix from raw data¶

The Compute raw data covariance… menu item pops up a dialog which specifies a time range for raw data covariance matrix estimation and the file to hold the result. If a covariance matrix is computed in this way, the rejection parameters specified in averaging preferences are in effect. For description of the rejection parameters, see Averaging preferences. The time range can be also selected interactively from the main raw data display by doing a range selection with shift left button drag.

Creating a new SSP operator¶

The Create a new SSP operator… menu choice computes a new SSP operator as discussed in Estimation of the noise subspace.

Time range specification for SSP operator calculation

When Create a new SSP operator… selected, a window shown in Time range specification for SSP operator calculation is popped up. It allows the specification of a time range to be employed in the calculation of a raw data covariance matrix. The time range can be also selected interactively from the main raw data display by doing a range selection with shift left button drag. Normally, you should use empty room data for this computation. For the estimation of the covariance matrix any existing projection will be temporarily switched off. Remember to inspect your data for bad channels and select an appropriate filter setting before creating a new SSP operator. The artifact rejection parameters specified averaging preferences will be applied in the covariance matrix calculation, see Averaging preferences.

Instead of using continuous raw data, it is also possible to employ short epochs around triggers (events) in the calculation of the new SSP operator by specifying a positive event number in the time specification dialog. This option is very useful, e.g., to remove MCG/ECG artifacts from the data to facilitate detection of epileptic spikes:

• Select left or right temporal channels to the display.
• Mark several peaks of the MCG signal in the data: click on the first one and control click on the subsequent ones to extend the selection.
• Select an event number next to the Picked to button in the tool bar, see The tool bar, and click Picked to . As a result the lines marking the events will change color (by default from green to blue) indicating transition to user-created events.
• Specify an epoch time range to be employed and the event number selected in the previous step for the SSP operator calculation.

Once the parameters are set, click Compute to calculate a covariance matrix according to you your specifications. Once the covariance matrix is ready, the parts corresponding to magnetometer or axial gradiometer, planar gradiometer, and EEG channels are separated and the corresponding eigenvectors and eigenvalues are computed. Once complete, a projection selector with eight magnetometer eigenvectors, five planar gradiometer eigenvectors, three EEG eigenvectors, as well as the existing projection items is displayed.

Using the projection selector, you can experiment which vectors have a significant effect on the noise level of the data. You should strive for using a minimal number of vectors. When the selection is complete, you can click Accept to introduce this selection of vectors as the new projection operator. Discard abandons the set of calculated vectors. Whenever EEG channels are present in the data, a projection item corresponding to the average EEG reference is automatically added when a new projection operator is introduced. More information on the SSP method can be found in The Signal-Space Projection (SSP) method.

Browsing data¶

If the strip-chart display has the input focus (click on it, if you are unsure) the keyboard and mouse can be used to browse the data as follows:

Up and down arrow keys

Activate the previous or next selection in the selection list.

Left and right arrow keys

If a single time point is selected (green line), move the time point forward and backward by \(\pm 1\) ms. If the shift key is down, the time point is moved by \(\pm 10\) ms. If the control key is down (with or without shift), the time point is moved by \(\pm 100\) ms. If mne_browse_raw is controlling mne_analyze (see Interacting with mne_analyze), the mne_analyze displays will be updated accordingly. If the picked time point falls outside the currently displayed section of data, the display will be automatically scrolled backwards or forwards as needed.

Rotate the mouse wheel or rotate the trackball up/down

Activate the previous or next selection in the selection list.

Rotate the trackball left/right or rotate the wheel with shift down

Scroll backward or forward in the data by one screen. With Alt key (Command or Apple key in the Mac keyboard), the amount of scrolling will be \(1\) s instead of the length of one screen. If shift key is held down with the trackball, both left/right and up/down movements scroll the data in time.

Overview¶

In mne_browse_raw and mne_process_raw events mark interesting time points in the data. When a raw data file is opened, a standard event file is consulted for the list of events. If this file is not present, the digital trigger channel, defined by the –digtrig option or the MNE_TRIGGER_CH_NAME environment variable is scanned for events. For more information, see the command-line references for mne_browse_raw and mne_process_raw.

In addition to the events detected on the trigger channel, it is possible to associate user-defined events to the data, either by marking data points interactively as described in Defining annotated events or by loading event data from files, see Loading and saving event files. Especially if there is a comment associated with a user-defined event, we will sometimes call it an annotation.

If a data files has annotations (user-defined events) associated with it in mne_browse_raw , information about them is automatically saved to an annotation file when a data file is closed, i.e., when you quit mne_browse_raw or load a new data file. This annotation file is called <raw data file name without fif extension> -annot.fif and will be stored in the same directory as the raw data file. Therefore, write permission to this directory is required to save the annotation file.

Both the events defined by the trigger channel and the user-defined events have three properties:

• The time when the event occurred.
• The value on the trigger channel just before the change and now. For user-defined events the value before is always zero and the current value is user defined and does not necessarily reflect a change on the trigger channel. The trigger channel events may also indicate changes between two non-zero values and from a non-zero to zero. The event list described in The event list shows only transitions from zero to a non-zero value. Similarly, the Jump to item in the tool bar, described in The tool bar, only detects transitions from zero to a nonzero value.
• An optional comment text, which is especially helpful in associating user-defined events with real-world activity, e.g., the subject closing or opening his/her eyes or an epileptic patient showing indications of a seizure.

The event list¶

The Windows/Show event list… menu choice shows a window containing a list of currently defined events. The list can be restricted to user-defined events by checking User-defined events only . When an event is selected from the list, the main display jumps to the corresponding time. If a user-defined event is selected, it can be deleted with the Delete a user-defined event button.

Loading and saving event files¶

Using the Load/Save events choices in the file menu, events can be saved in text and fif formats, see Event files, below. The loading dialogs have the following options:

Match comment with

Only those events which will contain comments and in which the comment matches the entered text are loaded. This filtering option is useful, e.g., in loading averaging or covariance matrix computation log files, see Common parameters and Common parameters. If the word omit is entered as the filter, only events corresponding to discarded epochs are loaded and the reason for rejection can be investigated in detail.

Add as user events

Add the events as if they were user-defined events. As a result, the annotation file saved next time mne_browse_raw closes this raw file will contain these events.

Keep existing events

By default, the events loaded will replace the currently defined ones. With this option checked, the loaded event will be merged with the currently existing ones.

The event saving dialogs have the following options controlling the data saved:

Save events read from the data file

Save only those event which are not designated as user defined. These are typically the events corresponding to changes in the digital trigger channel. Another possible source for these events is an event file manually loaded without the Add as user events option.

Save events created here

Save the user-defined events.

Save all trigger line transitions

By default only those events which are associate with a transition from zero to non-zero value are saved. These include the user-defined events and leading edges of pulses on the trigger line. When this option is present, all events included with the two above options are saved, regardless the type of transition indicated (zero to non-zero, non-zero to another non-zero value, and non-zero value to zero).

• Load the event file with the option Add as user events set.
• Open another data file or quit mne_browse_raw .
• Optionally remove unnecessary events using the event list dialog.

The directory in which the raw data file resides now contains an annotation file which will be automatically loaded each time the data file is opened. A text format event file suitable for this purpose can be created manually, extracted from an EDF+ file using the --tal option in mne_edf2fiff, or produced by custom software used during data acquisition.

Defining annotated events¶

The Windows/Show annotator… shows a window to add annotated user-defined events. In this window, the buttons in first column mark one or more selected time points with the event number shown in the second column with an associated comment specified in the third column. Marking also occurs when return is pressed on any of the second and third column text fields.

When the dialog is brought up for the first time, the file $HOME/.mne/mne_browse_raw.annot is consulted for the definitions of the second and third column values, i.e., event numbers and comments. You can save the current definitions with the Save defs button and reload the annotation definition file with Load defs . The annotation definition file may contain comment lines starting with ‘%’ or ‘#’ and data lines which contain an event number and an optional comment, separated from the event number by a colon.

Event files¶

A text format event file contains information about transitions on the digital trigger line in a raw data file. Any lines beginning with the pound sign (# ) are considered as comments. The format of the event file data is:

<sample> <time> <from> <to> <text>

where

** <sample>**

is the sample number. This sample number takes into account the initial empty space in a raw data file as indicated by the FIFF_FIRST_SAMPLE and/or FIFF_DATA_SKIP tags in the beginning of raw data. Therefore, the event file contents are independent of the Keep initial skip setting in the open dialog.

** <time>**

is the time from the beginning of the file to this sample in seconds.

** <from>**

is the value of the digital trigger channel at <sample> -1.

** <to>**

is the value of the digital trigger channel at <sample> .

** <text>**

is an optional annotation associated with the event. This comment will be displayed in the event list and on the message line when you move to an event.

When an event file is read back, the <sample> value will be primarily used to specify the time. If you want the <time> to be converted to the sample number instead, specify a negative value for <sample> .

Each event file starts with a “pseudo event” where both <from> and <to> fields are equal to zero.

Overall format¶

Any line beginning with the pound sign (#) in this description file is a comment. Each parameter in the description file is defined by a keyword usually followed by a value. Text values consisting of multiple words, separated by spaces, must be included in quotation marks. The case of the keywords in the file does not matter. The ending .ave is suggested for the average description files.

The general format of the description file is:

average {
    <common parameters>
    category {
        <category definition parameters>
    }

    ...
}

The file may contain arbitrarily many categories. The word category interchangeable with condition .

Common parameters¶

The average definition starts with the common parameters. They include:

outfile <*name*>

The name of the file where the averages are to be stored. In interactive mode, this can be omitted. The resulting average structure can be viewed and stored from the Manage averages window.

eventfile <*name*>

Optional file to contain event specifications. If this file is present, the trigger events in the raw data file are ignored and this file is consulted instead. The event file format is recognized from the file name: if it ends with .fif , the file is assumed to be in fif format, otherwise a text file is expected. The text event file format is described in Event files.

logfile <*name*>

This optional file will contain detailed information about the averaging process. In the interactive mode, the log information can be viewed from the Manage averages window.

gradReject <*value / T/m*>

Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the gradiometer channels, the epoch will be omitted from the average.

magReject <*value / T*>

Rejection limit for MEG magnetometer and axial gradiometer channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the magnetometer or axial gradiometer channels, the epoch will be omitted from the average.

eegReject <*value / V*>

Rejection limit for EEG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the EEG channels, the epoch will be omitted from the average.

eogReject <*value / V*>

Rejection limit for EOG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the EOG channels, the epoch will be omitted from the average.

ecgReject <*value / V*>

Rejection limit for ECG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the ECG channels, the epoch will be omitted from the average.

gradFlat <*value / T/m*>

Signal detection criterion for MEG planar gradiometers. The peak-to-peak value of all planar gradiometer signals must exceed this value, for the epoch to be included. This criterion allows rejection of data with saturated or otherwise dysfunctional channels. The default value is zero, i.e., no rejection.

magFlat <*value / T*>

Signal detection criterion for MEG magnetometers and axial gradiometers channels.

eegFlat <*value / V*>

Signal detection criterion for EEG channels.

eogFlat <*value / V*>

Signal detection criterion for EOG channels.

ecgFlat <*value / V*>

Signal detection criterion for ECG channels.

stimIgnore <*time / s*>

Ignore this many seconds on both sides of the trigger when considering the epoch. This parameter is useful for ignoring large stimulus artefacts, e.g., from electrical somatosensory stimulation.

fixSkew

Since the sampling of data and the stimulation devices are usually not synchronized, all trigger input bits may not turn on at the same sample. If this option is included in the off-line averaging description file, the following procedure is used to counteract this: if there is a transition from zero to a nonzero value on the digital trigger channel at sample \(n\), the following sample will be checked for a transition from this nonzero value to another nonzero value. If such an event pair is found, the two events will be jointly considered as a transition from zero to the second non-zero value. With the fixSkew option, mne_browse_raw/mne_process_raw behaves like the Elekta-Neuromag on-line averaging and Maxfilter (TM) software.

name <*text*>

A descriptive name for this set of averages. If the name contains multiple words, enclose it in quotation marks “like this”. The name will appear in the average manager window listing in the interactive version of the program and as a comment in the processed data section in the output file.

Category definition¶

A category (condition) is defined by the parameters listed in this section.

event <*number*>

The zero time point of an epoch to be averaged is defined by a transition from zero to this number on the digital trigger channel. The interpretation of the values on the trigger channel can be further modified by the ignore and mask keywords. If multiple event parameters are present for a category, all specified events will be included in the average.

ignore <*number*>

If this parameter is specified the selected bits on trigger channel values can be mask (set to zero) out prior to checking for an existence of an event. For example, to ignore the values of trigger input lines three and eight, specify ignore 132 (\(2^2 + 2^7 = 132\)).

mask <*number*>

Works similarly to ignore except that a mask specifies the trigger channel bits to be included. For example, to look at trigger input lines one to three only, ignoring others, specify mask 7 (\(2^0 + 2^1 + 2^2 = 7\)).

prevevent <*number*>

Specifies the event that is required to occur immediately before the event(s) specified with event parameter(s) in order for averaging to occur. Only one previous event number can be specified.

prevignore <*number*>

Works like ignore but for the events specified with prevevent . If prevignore and prevmask are missing, the mask implied by ignore and mask is applied to prevevent as well.

prevmask <*number*>

Works like mask but for the events specified with prevevent . If prevignore and prevmask are missing, the mask implied by ignore and mask is applied to prevevent as well.

nextevent <*number*>

Specifies the event that is required to occur immediately after the event(s) specified with event parameter(s) in order for averaging to occur. Only one next event number can be specified.

nextignore <*number*>

Works like ignore but for the events specified with nextevent . If nextgnore and nextmask are missing, the mask implied by ignore and mask is applied to nextevent as well.

nextmask <*number*>

Works like mask but for the events specified with nextevent . If nextignore and nextmask are missing, the mask implied by ignore and mask is applied to nextevent as well.

delay <*time / s*>

Adds a delay to the time of the occurrence of an event. Therefore, if this parameter is positive, the zero time point of the epoch will be later than the time of the event and, correspondingly, if the parameter is negative, the zero time point of the epoch will be earlier than the event. By default, there will be no delay.

tmin <*time / s*>

Beginning time point of the epoch.

tmax <*time / s*>

End time point of the epoch.

bmin <*time / s*>

Beginning time point of the baseline. If both bmin and bmax parameters are present, the baseline defined by this time range is subtracted from each epoch before they are added to the average.

basemin <*time / s*>

Synonym for bmin.

bmax <*time / s*>

End time point of the baseline.

basemax <*time / s*>

Synonym for bmax.

name <*text*>

A descriptive name for this category. If the name contains multiple words, enclose it in quotation marks “like this”. The name will appear in the average manager window listing in the interactive version of the program and as a comment averaging category section in the output file.

abs

Calculate the absolute values of the data in the epoch before adding it to the average.

stderr

The standard error of mean will be computed for this category and included in the output fif file.

Overall format¶

Any line beginning with the pound sign (#) in this description file is a comment. Each parameter in the description file is defined by a keyword usually followed by a value. Text values consisting of multiple words, separated by spaces, must be included in quotation marks. The case of the keywords in the file does not matter. The ending .cov is suggested for the covariance-matrix description files.

The general format of the description file is:

cov {
    <*common parameters*>
    def {
        <*covariance definition parameters*>
    }
    ...
}

The file may contain arbitrarily many covariance definitions, starting with def .

Common parameters¶

The average definition starts with the common parameters. They include:

outfile <*name*>

The name of the file where the covariance matrix is to be stores. This parameter is mandatory.

eventfile <*name*>

Optional file to contain event specifications. This file can be either in fif or text format (see Event files). The event file format is recognized from the file name: if it ends with .fif , the file is assumed to be in fif format, otherwise a text file is expected. If this parameter is present, the trigger events in the raw data file are ignored and this event file is consulted instead. The event file format is described in Event files.

logfile <*name*>

This optional file will contain detailed information about the averaging process. In the interactive mode, the log information can be viewed from the Manage averages window.

gradReject <*value / T/m*>

Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the gradiometer channels, the epoch will be omitted from the average.

magReject <*value / T*>

Rejection limit for MEG magnetometer and axial gradiometer channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the magnetometer or axial gradiometer channels, the epoch will be omitted from the average.

eegReject <*value / V*>

Rejection limit for EEG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the EEG channels, the epoch will be omitted from the average.

eogReject <*value / V*>

Rejection limit for EOG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the EOG channels, the epoch will be omitted from the average.

ecgReject <*value / V*>

Rejection limit for ECG channels. If the peak-to-peak amplitude within the extracted epoch exceeds this value on any of the ECG channels, the epoch will be omitted from the average.

gradFlat <*value / T/m*>

Signal detection criterion for MEG planar gradiometers. The peak-to-peak value of all planar gradiometer signals must exceed this value, for the epoch to be included. This criterion allows rejection of data with saturated or otherwise dysfunctional channels. The default value is zero, i.e., no rejection.

magFlat <*value / T*>

Signal detection criterion for MEG magnetometers and axial gradiometers channels.

eegFlat <*value / V*>

Signal detection criterion for EEG channels.

eogFlat <*value / V*>

Signal detection criterion for EOG channels.

ecgFlat <*value / V*>

Signal detection criterion for ECG channels.

stimIgnore <*time / s*>

Ignore this many seconds on both sides of the trigger when considering the epoch. This parameter is useful for ignoring large stimulus artefacts, e.g., from electrical somatosensory stimulation.

fixSkew

Since the sampling of data and the stimulation devices are usually not synchronized, all trigger input bits may not turn on at the same sample. If this option is included in the off-line averaging description file, the following procedure is used to counteract this: if there is a transition from zero to a nonzero value on the digital trigger channel at sample \(n\), the following sample will be checked for a transition from this nonzero value to another nonzero value. If such an event pair is found, the two events will be jointly considered as a transition from zero to the second non-zero value.

keepsamplemean

The means at individual samples will not be subtracted in the estimation of the covariance matrix. For details, see Epochs. This parameter is effective only for estimating the covariance matrix from epochs. It is recommended to specify this option. However, for compatibility with previous MNE releases, keepsamplemean is not on by default.

Covariance definitions¶

The covariance definitions starting with def specify the epochs to be included in the estimation of the covariance matrix.

event <*number*>

The zero time point of an epoch to be averaged is defined by a transition from zero to this number on the digital trigger channel. The interpretation of the values on the trigger channel can be further modified by the ignore and mask keywords. If multiple event parameters are present in a definition, all specified events will be included. If the event parameter is missing or set to zero, the covariance matrix is computed over a section of the raw data, defined by the tmin and tmax parameters.

ignore <*number*>

If this parameter is specified the selected bits on trigger channel values can be mask (set to zero) out prior to checking for an existence of an event. For example, to ignore the values of trigger input lines three and eight, specify ignore 132 (\(2^2 + 2^7 = 132\)).

mask <*number*>

Works similarly to ignore except that a mask specifies the trigger channel bits to be included. For example, to look at trigger input lines one to three only, ignoring others, specify mask 7 (\(2^0 + 2^1 + 2^2 = 7\)).

delay <*time / s*>

Adds a delay to the time of the occurrence of an event. Therefore, if this parameter is positive, the zero time point of the epoch will be later than the time of the event and, correspondingly, if the parameter is negative, the zero time point of the epoch will be earlier than the time of the event. By default, there will be no delay.

tmin <*time / s*>

Beginning time point of the epoch. If the event parameter is zero or missing, this defines the beginning point of the raw data range to be included.

tmax <*time / s*>

End time point of the epoch. If the event parameter is zero or missing, this defines the end point of the raw data range to be included.

bmin <*time / s*>

It is possible to remove a baseline from the epochs before they are included in the covariance matrix estimation. This parameter defines the starting point of the baseline. This feature can be employed to avoid overestimation of noise in the presence of low-frequency drifts. Setting of bmin and bmax is always recommended for epoch-based covariance matrix estimation.

basemin <*time / s*>

Synonym for bmin.

bmax <*time / s*>

End time point of the baseline, see above.

basemax <*time / s*>

Synonym for bmax.

General concepts¶

Unlike many other noise-cancellation approaches, SSP does not require additional reference sensors to record the disturbance fields. Instead, SSP relies on the fact that the magnetic field distributions generated by the sources in the brain have spatial distributions sufficiently different from those generated by external noise sources. Furthermore, it is implicitly assumed that the linear space spanned by the significant external noise patters has a low dimension.

Without loss of generality we can always decompose any \(n\)-channel measurement \(b(t)\) into its signal and noise components as

Further, if we know that \(b_n(t)\) is well characterized by a few field patterns \(b_1 \dotso b_m\), we can express the disturbance as

where the columns of \(U\) constitute an orthonormal basis for \(b_1 \dotso b_m\), \(c_n(t)\) is an \(m\)-component column vector, and the error term \(e(t)\) is small and does not exhibit any consistent spatial distributions over time, i.e., \(C_e = E \{e e^T\} = I\). Subsequently, we will call the column space of \(U\) the noise subspace. The basic idea of SSP is that we can actually find a small basis set \(b_1 \dotso b_m\) such that the conditions described above are satisfied. We can now construct the orthogonal complement operator

and apply it to \(b(t)\) yielding

since \(P_{\perp}b_n(t) = P_{\perp}Uc_n(t) \approx 0\). The projection operator \(P_{\perp}\) is called the signal-space projection operator and generally provides considerable rejection of noise, suppressing external disturbances by a factor of 10 or more. The effectiveness of SSP depends on two factors:

• The basis set \(b_1 \dotso b_m\) should be able to characterize the disturbance field patterns completely and
• The angles between the noise subspace space spanned by \(b_1 \dotso b_m\) and the signal vectors \(b_s(t)\) should be as close to \(\pi / 2\) as possible.

If the first requirement is not satisfied, some noise will leak through because \(P_{\perp}b_n(t) \neq 0\). If the any of the brain signal vectors \(b_s(t)\) is close to the noise subspace not only the noise but also the signal will be attenuated by the application of \(P_{\perp}\) and, consequently, there might by little gain in signal-to-noise ratio. An example of the effect of SSP demonstrates the effect of SSP on the Vectorview magnetometer data. After the elimination of a three-dimensional noise subspace, the absolute value of the noise is dampened approximately by a factor of 10 and the covariance matrix becomes diagonally dominant.

Since the signal-space projection modifies the signal vectors originating in the brain, it is necessary to apply the projection to the forward solution in the course of inverse computations. This is accomplished by mne_inverse_operator as described in Inverse-operator decomposition. For more information on SSP, please consult the references listed in Signal-space projections.

EEG average electrode reference¶

In the computation of EEG-based source estimates, the MNE software employs the average-electrode reference, which means that the average over all electrode signals \(v_1 \dotso v_p\) is subtracted from each \(v_j\):

It is easy to see that the above equation actually corresponds to the projection:

where

Continuous raw data¶

If a covariance matrix of a raw data is computed the data are checked for artefacts in 200-sample pieces. Let us collect the accepted \(M\) samples from all channels to the vectors \(s_j,\ j = 1, \dotsc ,M\). The estimate of the covariance matrix is then computed as:

where

is the average of the signals over all times. Note that no attempt is made to correct for low frequency drifts in the data. If the contribution of any frequency band is not desired in the covariance matrix estimate, suitable band-pass filter should be applied.

For actual computations, it is convenient to rewrite the expression for the covariance matrix as

Epochs¶

The calculation of the covariance matrix is slightly more complicated in the epoch mode. If the bmin and bmax parameters are specified in the covariance matrix description file (see Covariance definitions), baseline correction is first applied to each epoch.

Let the vectors

be the samples from all channels in the baseline corrected epochs used to calculate the covariance matrix. In the above, \(P_r\) is the number of accepted epochs in category \(r\), \(N_r\) is the number of samples in the epochs of category \(r\), and \(R\) is the number of categories.

If the recommended --keepsamplemean option is specified in the covariance matrix definition file, the baseline correction is applied to the epochs but the means at individual samples are not subtracted. Thus the covariance matrix will be computed as:

where

If keepsamplemean is not specified, we estimate the covariance matrix as

where

and

which reflects the fact that \(N_r\) means are computed for category \(r\). It is easy to see that the expression for the covariance matrix estimate can be cast into a more convenient form

Subtraction of the means at individual samples is useful if it can be expected that the evoked response from previous stimulus extends to part of baseline period of the next one.

Combination of covariance matrix estimates¶

Let us assume that we have computed multiple covariance matrix estimates \(\hat{C_1} \dotso \hat{C_Q}\) with corresponding degrees of freedom \(N_1 \dotso N_Q\). We can combine these matrices together as

where

SSP information included with covariance matrices¶

If a signal space projection was on when a covariance matrix was calculated, information about the projections applied is included with the covariance matrix when it is saved. These projection data are read by mne_inverse_operator and applied to the forward solution as well as appropriate. Inclusion of the projections into the covariance matrix limits the possibilities to use the --bad and --proj options in mne_inverse_operator , see Inverse-operator decomposition.