= Tutorial 8: Fixing stimulation delays =
''Authors: Francois Tadel, Elizabeth Bock''

<<TableOfContents(2,2)>>

== Existing delays ==
The delays present in those recordings are documented on this page:  [[DatasetAuditory|MEG auditory dataset]].

 * '''Delay #1''':   Between the stim markers (channel UDIO001) and the moment where the   sound card plays the sound (channel UADC001). This is mostly due to the   software running on the computer (stimulation software, operating   system, sound card drivers, sound card electronics). The delay can be   measured from the recorded files by comparing the triggers in the two   channels: Delay''' between 11.5ms and 12.8ms''' (std = 0.3ms) This delay is '''not constant''', we will need to correct for it.

 * '''Delay #2''':   Between when the sound card plays the sound and when the subject   receives the sound in the ears. This is the time it takes for the   transducer to convert the analog audio signal into a sound, plus the   time it takes to the sound to travel through the air tubes from the   transducer to the subject's ears. This delay cannot be estimated from   the recorded signals: before the acquisition, we placed a sound meter at   the extremity of the tubes to record when the sound is delivered.  Delay '''between 4.8ms and 5.0ms''' (std = 0.08ms). At a sampling rate of 2400Hz, this delay can be considered '''constant''', we will not compensate for it.

 * '''Delay #3''': The CTF MEG systems have a constant delay of '''4 samples'''     between the MEG/EEG channels and the analog channels (such as the    audio signal UADC001), because of an anti-aliasing filtered that is    applied to the first and not the second. This translate here to a '''constant delay''' of '''1.7ms'''.

 * '''Delay #4''':   When correcting of delay #1, the process we use to detect the  beginning  of the triggers on the audio signal (UADC001) sets the  trigger in the  middle of the ramp between silence and the beep. We  "over-compensate"  the delay #1 by 1.7ms. This can be considered as '''constant delay '''of about '''-1.7ms'''.

 * '''Uncorrected delays''':   We will correct for the delay #1, and keep the other delays (#2, #3  and  #4). After we compensate for delay #1 our MEG signals will have a '''constant delay '''of about 4.9 + 1.7 - 1.7 = '''4.9 ms'''.   We decide not to compensate for those delays because they do not   introduce any jitter in the responses and they are not going to change   anything in the interpretation of the data.

== Stimulation triggers delay ==

=== Evaluation ===
 * Right-click on Run01/Link to raw file > '''Stim '''> Display time series (stimuls channel, UDIO001)
 Right-click on Run01/Link to raw file > '''ADC V''' > Display time series (audio signal generated, UADC001)

 * In the Record tab, set the duration of display window to '''0.200s'''.
 Jump to the third event in the "standard" category.

 * We can observe that there is a delay of about '''13ms'''  between the time where the stimulus trigger is generated by the  stimulation computer and the moment where the sound is actually played  by the sound card of the stimulation computer ('''delay #1'''). This is matching the documentation of the experiment in the first section of this tutorial.

  {{http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory?action=AttachFile&do=get&target=stim1.gif|stim1.gif|height="282",width="590",class="attachment"}}

=== Correction ===
 * '''Delay #1''':  We can detect the triggers from the analog audio signal (ADC V/UADC001)  rather than using the events already detected  by the CTF software from  the stim channel (Stim/UDIO001).
 * Drag and drop '''Run01 '''and '''Run02 '''to the Process1 box.
 * Add '''twice''' the process "'''Events > Detect analog triggers'''".
 Once with event name="standard_fix" and reference event="standard".
 Once with event name="deviant_fix" and reference event="deviant".
 Set the other options as illustrated below:

  {{http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory?action=AttachFile&do=get&target=stim2.gif|stim2.gif|class="attachment"}}
 * Open  Run01 (channel ADC V) to evaluate the correction that was performed by  this process. If you look at the third trigger in the "standard"  category, you can measure a 14.6ms delay between the original event  "standard" and the new event "standard_fix".

  {{http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory?action=AttachFile&do=get&target=stim3.gif|stim3.gif|height="151",width="570",class="attachment"}}
 * Open '''Run01''' to re-organize the event categories:
  * '''Delete '''the unused event categories: '''standard''', '''deviant'''.
  * '''Rename '''standard_fix and deviant_fix to '''standard''' and '''deviant'''.
 * Open '''Run02''' and do the same cleaning operations:

  {{http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory?action=AttachFile&do=get&target=stim5.gif|stim5.gif|height="149",width="502",class="attachment"}}
 * '''Important note''': We compensated for the jittered delays (delay #1), but not for the other ones (delays #2, #3 and #4). There is still a''' constant 5ms delay''' between the stimulus triggers ("standard" and "deviant") and the time where the sound actually reaches the subject's ears.