Tutorial 23: Scouts

Authors: Francois Tadel, Elizabeth Bock, John C Mosher, Richard Leahy, Sylvain Baillet

In Brainstorm jargon, a scout represents a region of interest (ROI) in the available source space. It is a subset of dipoles defined on the cortex surface or the head volume. This tutorial explains how to create one or several scouts, use them to represent the activity in specific brain regions and compare the responses between different experimental conditions.


For all the brain imaging experiments, it is highly recommended to have a clear hypothesis to test before starting the analysis of the recordings. With this auditory oddball experiment, we would like to explore the temporal dynamics of the auditory network, the deviant detection and the motor response. According to the literature, we expect to observe at least the following effects:

We will start by creating regions of interest corresponding to the auditory cortices to illustrate the tools, then define other regions to better explore the dynamics of the brain response.

Creating a scout

Almost all the features related to scout manipulation are accessible in the Scout tab in the main Brainstorm window. The scouts are automatically saved in the surface file from which they are created, and they are loaded and automatically displayed each time the surface is loaded.

An atlas designates, in this context, a list of scouts. For one cortex surface, we can have as many atlases as needed. An atlas can be an anatomical parcellation (like the ones loaded when using FreeSurfer), a random parcellation generated by Brainstorm, or a user-defined list of ROIs. All the surfaces contain, by default, an empty atlas called "User scouts", for the user to create new regions of interest.

First vertex (seed)

Growing a scout

For now, our scout contains only one vertex of the cortex surface. Most of the time, the aim of a scout is to extract the average activity over a larger region. The buttons in the Scout size section offer basic operations to define the scout extension.

Grow the scout A1L to 20 vertices, not in constrained mode. You can read the number of vertices and the estimated cortical area just below the [<<] and [>>] buttons.

Display time series

Select the scout in the list, click on the second button in the toolbar [Display scouts time series]. It displays the signal associated with this region for the entire time window (-100ms to 500ms).
We can now observe the early response at 50ms (P50) that was not very obvious before.

3D display options

In the toolbar on the right side of the scouts list, you can find a list display options. Leave your mouse over each button for a few seconds to get a short description.

Scout function

We have extended the scout A1L to 20 vertices. Because this is a source model with constrained dipoles orientations, we have one source only per vertex. The region A1L corresponds to 20 signals.

The signals are grouped together into one unique signal that is then used to represent the activity of the region of interest. In the list of available scouts, you can see the indication [Mean] next to the name of the scout. It represents the name of the function that is used for combining all the source signals into one. This function can be changed individually for each scout, with the menu Scout > Set function.

Here is a description of the different options. In the case of unconstrained sources (3 signals for each vertex, one for each orientation), the function is applied separately for each orientation and produces 3 time series instead of one. For more details, see the code of bst_scout_value.m.

Option: Absolute / relative

As said in the previous tutorial, the minimum norm current amplitudes can be positive or negative depending on the dipole orientation. This means that the values of the scouts, depending on the function that is used, may be positive or negative too. Most of the time we are interested in visualizing the absolute values of the scouts time series, to compare the activation level in different conditions or subjects. But it is sometimes easier to understand the temporal dynamic of a ROI with the relative values.

At the bottom of the Scout tab, you can choose to display either Absolute or Relative values.
The effect of this options changes whether you are processing source files with constrained (1 signal per vertex) or unconstrained (3 signals per vertex) dipoles orientations:

Constrained: Apply the scout function to all source signals, then:

Unconstrained: Apply the scout function to the source signals for each orientation (Sx,Sy,Sz) separately, and then returns either the norm of the 3 orientations, or each orientation separately:

Display only: Note that this relative/absolute selection is a display option, it is not saved in the scouts themselves. It is used only when displaying the scouts time series with the [Display scouts time series] button of the Scout tab. In all other cases, such as the extraction of the scouts values from a script, this relative/absolute option is ignored.

Multiple conditions

We can easily compare the activity between multiple conditions and multiple regions of interest.

Other regions of interest


Multiple scouts

We can display the activity of multiple regions simultaneously.


From the database explorer

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 database explorer. It means that you can quickly compare the values for a scout between many different conditions without having to open them all.


Sign flip

In the case of source models with constrained orientations (normal to the cortex), the sign of the current can be an issue. If the region is large enough to include vertices with normals in opposite directions, averaging the source values may cancel out the activity.

Let's use the example from the previous tutorial and consider that one scout contains all the dipoles corresponding to both the red arrows (positive values) and the blue arrows (negative values). If we average all the values from this scout, we get a value close to zero.

To avoid this, a mechanism was added in the scout calculation, to flip the sign of sources with opposite directions before the averaging. We start by finding the dominant orientation of the scout, then flip the sign of the values that are not in the same direction (scalar product of the orientations < 0).

If the sign of some sources is flipped, you get a message in the Matlab command window, for example:
BST> Flipped the sign of 7 sources.


Scout toolbar and menus


Scout region

A scout is defined by its name, and it has several properties: a list of vertices and an aggregating function. These are usually enough to explore the activity at the cortex level the way we did it in these tutorials. An extra property can be defined on the scout: the explicit classification in a brain region. This property is used only in more advanced functional connectivity analysis, for the representation of the NxN connection graphs. It is introduced here for reference purpose.

A brain region in Brainstorm is following a hierarchy with three levels: hemisphere / lobe / sub-region. The definition at each level is optional: a region can be classified only at the hemisphere level, or at the hemisphere+lobe level, or none of them. It depends on level or hierarchy you are interested in to explore the connectivity graphs.

The region for a scout can be set with the Scout > Set region menus, and is encoded in a string that contains at least 2 characters: "HLxxx". H represents the hemisphere (L,R,U), L stands for the lobe (F,PF,C,P,T,O,L,U), and xxx for the sub-region name (optional). For both the hemisphere and the lobe, the value "U" stands for "Undefined", meaning that the classification is simply not set. The menu Set region>Custom region... lets you directly edit this string.

When set, the region string is shown before the scout name in the list, representing only the defined levels. It doesn't show the letters U for "undefined".


On the hard drive

The scouts are saved in the surface file on which they have been defined.
In the anatomy view, right-click on the selected cortex surface (cortex_15002V) > View file contents.


iAtlas: Index of the atlas that is currently selected for this surface.

Atlas: Array of structures, each entry is one menu in the drop-down list in the Scout tab.

Useful functions

Additional documentation

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Tutorials/Scouts (last edited 2017-01-27 09:23:56 by FrancoisTadel)