= Tutorial 8: Scouts =
In Brainstorm jargon, a ''scout '' is a region of interest defined on the cortical surface: a subset of vertices of this surface. This document explains how to create one or several scouts, use them to retrieve the activity in specific brain regions, and compare between conditions.

<<TableOfContents(2,2)>>

== Creating a scout ==
Almost all the features related to the scouts manipulation are accessible in the ''Scout'' tab in the 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 / Right / ERF'' (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 ''Scout'' tab, click on the first button in the toolbar (the 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:firstScout.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''.
 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 furthest vertex (respect to the seed) from the current scout.
 * ''''>>'''': Grow scout in all directions
 * ''''<<'''': Shrink scout in all directions
 * ''''Constrained'''': 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 in the toolbar), and then '''select again''' the "LeftSS" scout. All the points you would click on the cortex would be added to the selected scout.

Now: add about 20 vertices with button '>>', '''not '''in ''Constrained ''mode, and display the scout values again. 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.

{{attachment:scoutGrow.gif}}

== Multiple scouts ==
We are going to create an other scout for the other condition: the stimulation of the left thumb.

 1. Close all figures (toolbar button).
 1. Display the times series for ''Subject01 / Left / ERF'' (double-click).
 1. Display the associated sources (Ctrl+S).
 1. Go to the main response peak (46 ms).
 1. Adjust the threshold value to get only a very focal point (about 85%).
 1. Create a new scout at this point. Name it ''RightSS'', for Right Somato-Sensory cortex.
 1. Grow it to the same number of vertices as the ''LeftSS ''scout (about 15 vertices).
 1. Select both scouts (Ctrl+click) and click on ''Display scouts time series'' button (second button in toolbar).<<BR>><<BR>> {{attachment:scouts2.gif}} <<BR>><<BR>> {{attachment:scoutsTS_LR.gif}}
 1. You can also display the values of the two scouts on the same graph. Just check the ''Overlay > Scouts'' checkbox in the Scout tab.<<BR>><<BR>> {{attachment:scoutsTS_LR_overlay.gif}}
 1. You can observe something that we expected: the activity in the '''right somatosensory cortex''' is much higher than in the left somatosensory cortex for a stimulation of the '''left thumb'''.

== Load/Save scouts ==
In case you close the Brainstorm window, delete or unload your scouts (and this will happen in the next few minutes), save the scouts before going further.

 * Select both scouts at the same time (Ctrl+click), and click the ''Save scouts'' button.<<BR>><<BR>> {{attachment:saveScouts.gif}}
 * All the scouts will be saved in the same .mat file, in the subject's anatomy folder (same directory as the MRI and surfaces).
 * To load them later, just click the ''Load scouts'' button, and select the file.

== Display scouts time series from the database tree ==
You have to display the sources on the cortex to create the scouts. But once they are created, you can directly display the scouts time series from the tree. It means that you can quickly compare the values for a scout between many different conditions without having to open them all.

 1. Close all the figures (button in toolbar).
 1. Select the first scout (LeftSS)
 1. Right-click on the sources file for Right condition > Cortical activations > Scouts time series.<<BR>><<BR>> {{attachment:treeRight.gif}} - {{attachment:treeRight_TS.gif||height="152",width="269"}}
 1. You can also display many sources files at the same time. Try doing the same selecting both results file at the time<<BR>><<BR>> {{attachment:treeLR.gif}} - {{attachment:treeLR_TS.gif||height="132",width="272"}}
 1. You can superimpose the two traces by selecting the ''Overlay > Conditions'' checkbox in ''Scout ''panel.<<BR>><<BR>> {{attachment:panelOverlayCond.gif||height="98",width="176"}}
 1. This menu "Scouts time series" is present at all the levels. Try right-clicking on Subject01.<<BR>><<BR>> {{attachment:treeSubj.gif}} - {{attachment:treeSubj_TS.gif||height="164",width="291"}}
 1. If you select a node in the database tree and click on the ''Display scouts time series'' button in the ''Scout ''tab, it would have exactly the same effect. <<BR>>Try selecting '''both scouts''' in the list, select '''Subject01 '''in the tree, and then click on this button. You will observe the reponse for each scout in both conditions.<<BR>><<BR>> {{attachment:scoutsOverlayBoth.gif}}

== 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. If you delete or alter the scouts LeftSS and RightSS: just reload them from the file you've just created.

=== 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.
  * Define the 3D mask using the different drawing tools.
  * Adjust the MRI contrast with right-click+move on the MRI image.
  * Move throught the slices with the mouse wheel, the small image on the lift, or the slider.
  * Once you are done, click on ''Ok''. A new scout is created, including all the vertices that are located inside the 3D mask.
  * __Warning__: The 3D mask is reinterpolated on the surface, all the volume information is lost. It means that the mask you intedend to draw might be really different from what you get as a scout at the end...<<BR>><<BR>> {{attachment:menuEditMriMask.gif}}
 * '''Find maximal value''': Find the vertex with the maximal intensity at the current time, and create a scout centered on it.
 * You can delete all the scouts you have created by selecting them and pressing ''Delete ''key.<<BR>>

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

 * '''Rename''': Rename the selected scout. <<BR>>Shortcut: double-click.
 * '''Set color''': Change the display color of scout patch in 3D figures.
 * '''Remove''': Delete selected scouts.
 * '''Merge''': Join two or more selected scouts.
 * '''Deselect all''': Deselect all the scouts in the list.<<BR>>Shortcut:Escape key.
 * '''Add vertices''': The user can select some points on the cortex surface and add them to the scout.<<BR>>Equivalent:Click on ''Select point'' (first toolbar button), then select the scout in list, and slect 3d points.
 * '''Edit in MRI''': Open the same interface as menu New > Define in MRI slices, in order to edit the scout.
 * '''Expand (correlation)''': Computes the correlation between the values at the scout's seed (first point) and all the other sources. The sources that have correlation coefficient superior to a given threshold are added to the scout. <<BR>>Correlation is computed with the Matlab ''corrcoef ''function.
 * '''Find maximal value''': Move the scout's seed to the source that has the maximum amplitude '''in the scout''', at current time.
 * '''Remove vertices''': Remove the scout's vertices permanently from the cortex surface. <<BR>>__Warning__: This is a menu that can be used only when defining the subject's anatomy. Never do that if you already have headmodels or sources based on this surface...
 * '''Simulation''': Forward model of selected scouts. Simulate the scalp data that would be recorded if only the selected cortex region was activated. Create a new "source" file in the database.<<BR>>If no scout is selected: simulate recordings produced by the activity of the whole cortex.

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

 * '''View time series''': Same as the ''View time series'' button i nthe toolbar.
 * '''View on cortex''': Open a 3D figure with the cortex and the selected scout (if such a figure does not exist yet).
 * '''View in MRI Viewer''': Display the scout as a 3D mask in the MRI Viewer (anatomy only, no sources information)<<BR>><<BR>> {{attachment:scoutInMriViewer.gif}}
 * '''Center MRI on scout''': When a MRI figure (3D or MRI Viewer) is opened: center view on the scout's seed.

=== Menu: View > 3D display options ===
 . To test this menu: open first a view of the sources in the MRI Viewer.<<BR>>Right-click on sources file > Cortical activations > Display on MRI (MRI Viewer), and go to intersting time point (around 45ms), and slices (around somato-sensory cortex).

 . {{attachment:menuDisplayOptions.gif}}

 * '''Show selected scouts''': If selected, only the scouts that are selected are displayed in the 3D figures. Useful when you have many scouts defined, or if you want to produce MRI images with just one area coloured.
 * '''Show all scouts''': If selected, all the scouts are displayed in all the figures, whether they are selected or not. Default.
 * '''Show scout patch''': Display full scout patch in MRI/3D figures. If not selected: display only the seed of the scout.
 * '''Limit MRI sources to scouts''': In all MRI views: display only sources values for the visible scouts. If not selected, display the sources for all the cortical surface.<<BR>><<BR>> {{attachment:mriSelScout.gif}} ON<<BR>><<BR>> {{attachment:mriAll.gif}} OFF

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

 * '''Relative / Absolute values''': Extract to the sources values in absolute or relative values (before applying any other function).

 * '''Sources''': ... : Selection of the function to apply to the values of all the sources included in a scout. ''Mean'', ''Max'', ''PCA ''and ''Power ''return only one value per time (taking for instance the average of all the sources), while ''All ''displays the time series for sources in the scout. This last menu is not available when more than one condition or scout is selected.

 * Try all the configurations for the scout '''LeftSS '''on condition '''Right'''.

||Absolute / Mean: || {{attachment:optionsMean.gif}} ||
||Absolute / Max: <<BR>>(same shape, higher amplitudes) || {{attachment:optionsMax.gif}} ||
||Absolute / Power: || {{attachment:optionsPower.gif}} ||
||Absolute / PCA: <<BR>><<BR>>Compute the first mode of PCA of time series within each scout region || {{attachment:optionsPCA.gif}} ||
||Relative / Mean: || {{attachment:optionsRelative.gif}} ||


== Next ==
Next step, the [[Tutorials/TutProcesses|Processes tab]].