= Tutorial 15: Source estimation =
''Authors: Francois Tadel, Elizabeth Bock, John C Mosher, Sylvain Baillet''

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From continuous tutorials:

== Inverse model ==
Right-click on ''(Common files)'', on the head model or on the subject  node, and select "'''Compute sources'''". A shared inversion kernel is created in ''(Common files)'';  a link node is now visible for each recordings file, single  trials and  averages. For more information about what those links mean  and the  operations performed to display them, please refer to the [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation|tutorial #8 "Source estimation"]].

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=inverseDb.gif|inverseDb.gif|class="attachment"}}

== Explore the sources ==
Right-click on the sources for the left average > Cortical activations > '''Display on cortex''', or simply double click on the file. Go to the main response peak at '''t = 30ms''', and increase the '''amplitude threshold''' to '''100%'''.  You see a strong activity around the right primary somatosensory  cortex, but there are still lots of brain areas that are shown in plain  red (value >= 100% maximum of the colorbar ~= 280 pA.m).

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=inverse100.gif|inverse100.gif|class="attachment"}}

The  colorbar maximum is set to an estimation of the maximum source  amplitude over the time. This estimation is done by finding the time  instant with the highest global field power on the sensors (green trace  GFP), estimating the sources for this time only, and then taking the  maximum source value at this time point. It is a very fast estimate, but  not very reliable; we use it because calculating the full source matrix  (all the time points x all the sources)  just for finding the maximum  value would be too long.

In  this case, the real maximum is probably higher than what is used by  default. To redefine the colorbar maximum: right-click on the 3D figure  > '''Colormap: sources > Set colorbar max value'''. Set the maximum to '''480 pA.m''', or any other value that would lead to see just one very focal point on the brain at 30ms.

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=inverse480.gif|inverse480.gif|class="attachment"}}

Go back to the first small peak at '''t=16ms''', and lower the threshold to '''10%'''.  Then do what you did with at the sensor level: follow the information  processing in the brain until 100ms, millisecond by millisecond,  adapting the threshold and the camera position when needed:

 * '''16 ms''' (top-left): First response, primary somatosensory cortex (S1 right)
 * '''30 ms''' (top-right): S1 right
 * '''60 ms''' (bottom-left): Secondary somatosensory cortex (S2 right)
 * '''70 ms''' (bottom-right): Activity ipsilateral to the stimulus (S2 left + S2 right)

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=sources16.gif|sources16.gif|class="attachment"}} {{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=sources30.gif|sources30.gif|class="attachment"}}

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=sources60.gif|sources60.gif|class="attachment"}} {{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg?action=AttachFile&do=get&target=sources70.gif|sources70.gif|class="attachment"}}

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