= Tutorial 15: Import epochs =
''Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet''

We can consider that our datasets are clean from any major artifact. We will now proceed to the analysis of the brain signals we recorded in response to the auditory stimulation. There are two major types of processing workflows for MEG/EEG, depending on whether we are dealing with an event-related paradigm or a steady-state/resting-state study.

This tutorial will only focus on the event-related case: series of stimuli are sent to the subject and we have the corresponding triggers marked in the recordings. We will base our analysis on those triggers, import short epochs around each of them and average them. You will find in the advanced tutorials a scenario of MEG resting-state analysis.

<<TableOfContents(2,2)>>

== Import in database ==
Until now, we've only been looking at data that was read from continuous files. The raw file  viewer provides a rapid access to the  recordings, but many  operations can only be applied to short segments of recordings that have been imported in the database, called "epochs" or "trials".

 * Right-click on '''Run#01''' > '''Import in database'''. <<BR>><<BR>> {{attachment:import_popup.gif||height="152",width="298"}}
 * Set the import options as they as described below:  <<BR>><<BR>> {{attachment:import_options.gif||height="366",width="587"}}

 * '''Time window''':   Time range of interest. We are interested by all the stimulations, so   do not change this parameter; the default values always represent the   entire file.
 * '''Split''':  Useful to  import continuous recordings without events, to import  successive  chunks of the same duration. We do not need this here.
 * '''Events selection''':    Check the "Use events" option, and select both "'''standard'''" and "'''deviant'''".  <<BR>>The  number between parenthesis represents the number of occurrences of each event in the selected time window (changes if you modify the  time  definition at the top of the window)
 * '''Epoch time''':  Time segment that is extracted around each event marker. Set it to '''[-100,+500]ms'''.
 * '''Apply SSP/ICA projectors''': Use the active SSP projectors calculated during the previous pre-processing steps. Always check the summary of the projectors that are selected. <<BR>>Here there are 2 categories ("cardiac" and "blink") with a total of 3 projectors selected (one in "cardiac" and two in "blink", the blink and the saccade).  Keep this option selected.
 * '''Remove DC Offset''':   Check this option, select '''Time range: [-100, 0] ms'''. For each epoch, it will:
  * Compute the average of each channel over the  baseline   (pre-stimulus interval: [-100,0]ms)
  * Subtract it from  the   channel at every time instants (full epoch interval: [-100,+500]ms).
  * This option removes the baseline value of each sensor. In MEG, the sensors record variations around a    somewhat arbitrary level, therefore this operation is always needed,    unless it was already applied during one of the pre-processing steps.
  * Note that a high-pass filter with a very low frequency (for instance    0.3Hz) can replace efficiently this DC correction. If a high-pass filter    has already been applied to the recordings, you may want to unselect    this option.
 * '''Resample recordings''': Keep this unchecked
 * '''Create a separate folder for each epoch type''':  Do __not__ check this option.
  * If selected: a new folder is created for each event type ("standard" and "deviant")
  * If not   selected: all the epochs are saved in a new folder, the same one for all   the events, that has the same name as the initial raw file. This is what we want.
  * In this case, we have to select this second option because we have two acquisition runs with different channel files (different head positions and different SSP projectors) to import for the same subject. If we select this option, the "standard" epochs of both runs would be imported in the same folder and would end up sharing the same channel file, which is not correct because the channel files for both runs are different.

One new folder appear in Subject01.

 * It contains a channel file (copied from the continuous file) and two trial groups. To expand a group of trials and access the individual   epochs: double-click on it or click on the "+" next to it. <<BR>><<BR>> {{attachment:import_new_folder.gif||height="171",width="226"}}
 * The   SSP projectors calculated in the previous tutorial were applied on the   fly when reading from the continuous file. Those epochs are clean from   eye blinks and power line contamination.
 * Note that the trials that are overlapping with a BAD segment are tagged  as bad in the database explorer (marked with a red dot). All   the bad trials are going to be ignored in the rest of the  analysis,    because they are ignored by the Process1 and Process2 tabs (see next tutorial).  <<BR>><<BR>> {{attachment:import_bad.gif||height="100",width="232"}}

== Review the individual trials ==
After reviewing the continuous file with the "columns" view (channels one below the other) it can be useful to also review the imported trials with the "butterfly" view (all the channels superimposed).

 * Double-click on the first trial for the "deviant" condition.
 * Switch to the "butterfly" display mode: in the Record tab, click on the first button in the toolbar. <<BR>><<BR>> {{attachment:import_review.gif||height="172",width="440"}}
 * Right-click on the figure > Navigator > '''Next data file''', or use the keyboard shortcut '''F3'''. <<BR>>This way you can quickly review all the  trials  to make sure that there is no obvious problem.<<BR>>Mac users: The keys "Fx" are obtained by holding the "Fn" key simultaneously. <<BR>><<BR>> {{attachment:import_navigator.gif}}

To mark a trial as bad manually, you have three methods:

 * Right-click on the trial file in the database > '''Reject trial'''
 * Right-click on the figure > '''Reject trial'''
 * Use the keyboard shortcut '''Ctrl+B'''
 * To set all the trials back as good in a group: right-click on the trials group > Accept bad trials.

== Run #02 ==
Repeat the same operations for the second dataset:

 * Right-click on '''Run#02''' > '''Import in database'''.
 * Import events "standard" and "deviant" with the same options. <<BR>><<BR>> {{attachment:import_run02.gif||height="150",width="236"}}

<<TAG(Advanced)>>

== On the hard drive ==
Right-click on any imported epoch > File > View file contents:

 . {{attachment:import_struct.gif||height="418",width="477"}}

==== Structure of the imported epochs ====
 * '''F''': recordings time series (nChannels x nTime), in Volts.

 * '''Std''': Standard deviation or standard error, when available (see next tutorial).
 * '''Comment''': String displayed in the database explorer to represent this file.
 * '''ChannelFlag''': One value per channel, 1 means good, -1 means bad.
 * '''Time''': Time values for each sample recorded in F, in seconds.
 * '''DataType''': Type of the data saved in the F matrix.
 * '''Device''': Name of the acquisition system used to record this file.
 * '''nAvg''': For averaged files, number of trials that were used to compute this file.
 * '''Events''': Time markers available in the file (stimulus triggers or other events)
  * '''label''': Name of the event group.
  * '''color''': [r,g,b] Color used to represent the event group, in Matlab format.
  * '''epochs''':  [1 x Nevt] Indicate in which epoch the event is located (index in the  sFile.epochs array), or 1 everywhere for files that are not saved in  "epoched" mode.
 Nevt = number or occurrences of the event = number of markers in this group.
  * '''samples''': [1 x Nevt] Sample indices of each marker in this group (samples = times * sfreq).
 For extended events: [2 x Nevt], first row = start, second row = end.
  * '''times''': [1 x Nevt] Time in seconds of each marker in this group (times = samples / sfreq).
 For extended events: [2 x Nevt], first row = start, second row = end.
  * '''reactTimes''': Not used anymore
  * '''select''': Not used anymore
 * '''History''': Operations performed on file since it was imported (menu "View file history").

==== File history ====
Right-click on any imported epoch > File > View file history:

 . {{attachment:import_history.gif||height="197",width="603"}}

==== List of bad trials ====
 * There is no field in the file structure that says if the trial is good or bad.
 * This information is saved at the level of the folder, in the '''brainstormstudy.mat''' file.
 * Right-click on an imported folder > File > Show in file explorer.<<BR>><<BR>> {{attachment:import_folder.gif}}
 * Load the brainstormstudy.mat file into Matlab: <<BR>><<BR>> {{attachment:import_study.gif}}

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