= Tutorial 7: Scouts =
This tutorial uses Sabine Meunier's somatotopy experiment, called ''TutorialCTF ''in your Brainstorm database.

In Brainstorm jargon, a ''scout '' is a region of interest defined on the cortical surface, consisting  of a subset of vertices of this surface. This document explains how to create one or several scouts, use them to retrieve the activity in pre-defined brain regions, and compare between conditions.

<<TableOfContents(2)>>

== Creating a scout ==
Almost all the features related to the scouts manipulation are accessible in the Scouts tab in main Brainstorm window. We are going to use this panel to create a scout that includes the cortical area that we observed in the previous tutorial: the one that responds to the stimulation of the right thumb.

=== First vertex (seed) ===
 1. Select the protocol ''TutorialCTF'', and display the times series for ''Subject01 / !StimRightThumb / ERP'' (double-click).
 1. Display the associated sources (try it from the time series figure: Ctrl+S, or figure popup menu)
 1. Go to 46ms, and set the data threshold around 80%.
 1. Switch to the ''Scouts'' tab, click on the first button (a big cross), and then click in the middle of the red stain in left hemisphere in the 3D figure (rotate and zoom before if necessary). A small dot with the label "1" appears where you clicked. Your first scout is created, and contains only one vertex for the moment. It is now referenced in ''Available scouts'' list.<<BR>><<BR>> {{attachment:panelScouts.gif}} - {{attachment:scouts1.gif}}
 1. Rename the scout into "LeftSS", for left somatosensory cortex: double-click on it in the ''Available scouts'' list, or scouts menu ''Edit > Rename scout''.
 1. Click on the second button in the ''Scouts ''panel toolbar, tooltip: ''Display scouts time series''. And you will get the time course of this particular source for the whole time window (-50ms to 250ms).<<BR>><<BR>> {{attachment:scoutsTS1.gif}}

=== Growing a scout ===
In this case, the source is so focal that we could even use only the first vertex we selected to represent this area. But most of the time, the aim of a scout is to get the average activity of a larger region; so for the example, let's grow this scout.

 * The buttons in in the ''Scout size'' panel offer basic operations to define scout extension.
 * ''''>'''': Add the closest vertex (respect to the seed) to the current scout.
 * ''''<'''': Remove the farthest vertex (respect to the seed) from the current scout.
 * ''''>>'''': Grow scout in all directions
 * ''''<<'''': Shrink scout in all directions
 * ''''Contrained'''': If this button is pressed, only the vertices that have a sources value above the threshold will be added to the scout (its growth will be limited to the red patch on the surface).
 * Last method to add points to a scout: select the ''Select point'' button (big cross, first in toolbar), and then '''select '''again the "LeftSS" scout. All the points you will click on the cortex will be added to the selected scout.

For demonstration purpose, you can add about 30 vertices to scout ''LeftSS'', '''not '''in ''Constrained ''mode, and display it again.

 . {{attachment:scoutsLeftSS.gif}} -- {{attachment:scoutsTSLeftSS.gif}}

You can notice that the overall shape is the same as the scout with only one vertex, but the amplitudes are much lower. This is because the time series of all the sources in this scout have been averaged. And as we averaged the maximum values with lower values, the result is lower.<<BR>><<BR>>

== Scout toolbar and menus ==
Let's spend a few minutes to explore all the menus in the ''Scout ''tab. Please click on all of them, it's the best way to remember.

=== Menu: New ===
 . {{attachment:menuNew.gif}}

 * '''Define in 3D view''': Same as clicking on the first button of the toolbar (Select point / big cross).
 * '''Define in MRI slices''': Open an interface to draw a 3D ROI, slice by slice.
 * '''Find maximal value''': Find the vertex with the maximal intensity at the current time, and create a scout centered on it.

=== Menu: Edit ===
 . {{attachment:menuEdit.gif}}

=== Menu: View ===
 . {{attachment:menuView.gif}}

=== Menu: View > Display options ===
 . {{attachment:menuDisplayOptions.gif}}

=== Menu: View > Display options ===
 . {{attachment:menuTSOptions.gif}}

Configure scout

Display scouts time series from the tree