= Volume source estimation =
''Authors: Francois Tadel, John C Mosher''

The default approach for the source estimation in Brainstorm is to limit the source space to the cortex surface. This choice is motivated by the assumption that most of  the activity we record in MEG and EEG  comes from the cerebral cortex. Constraining the source reconstruction to a surface works well when this assumption is verified, and the results we obtain are much easier to review that a full volume.

However, when studying the activity from deeper regions of the brain or when processing recordings from patients with serious anatomical abnormalities, this cortical constraint is not always adapted. This tutorial explains how to construct a grid of dipoles that samples the full brain volume.

<<TableOfContents(2,2)>>

== Compute a volume head model ==
The example below uses the protocol TutorialIntroduction created in the [[http://neuroimage.usc.edu/brainstorm/Tutorials#Get_started|introduction tutorials]].

 * Select the protocol TutorialIntroduction . Go to the view "Functional data (sorted by subjects)".
 * In the imported Run01, right-click on the channel file > '''Compute head model '''> '''MRI volume'''. <<BR>>The various options available a described below.<<BR>><<BR>>  {{attachment:gridOptions.gif||height="420",width="673"}}

 * '''Generate from cortex surface''': Creates a grid that samples the head model in an adaptive way, denser at the surface of the brain (it is closer to the sensors therefore the expected spatial resolution of the MEG/EEG source estimation is higher), and sparser at the center of the brain. This grid is created with following algorithm:
  * Start with a brain envelope with a given number of vertices ('''Initial number of vertices''').
  * Shrink the previous layer, and downsample it by a given factor (option '''Downsampling factor''').
  * Repeat this operation ['''Number of layers'''] times, or until there are no more vertices.

 * '''Regular grid''': Creates a regular grid with one grid point every few millimeters (option Grid resolution). This grid is isotropic grid, ie. all the points are equally spaced.

 * '''Load from a file/variable''': If you already have a grid of points you would like to use, you can import it directly from a file or from a Matlab variable (only one field, [N,,points,,x3] values).

 * '''Use template grid''': This option is only available when a template source grid has been defined on the default anatomy. For more information, see tutorial [[http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects#Volume_source_models|Group analysis: Subject coregistration]].

 * '''Preview''': For each combination of parameters, you can see the total number of grid points at the bottom of the option window. Click on [Preview] to see the grid of dipoles. Screen captures below show an adaptive grid (left) and a regular grid (right). <<BR>><<BR>> {{attachment:grid.gif||height="259",width="652"}}
 * Leave all the intial options, and click on Ok. A new head model is computed. <<BR>><<BR>> {{attachment:treeHeadmodel.gif}}

== Compute sources ==
 * Make sure your new volume head model is selected as the default one (displayed in green).
 * Right-click on the volume head model > '''Compute sources [2016]''' > Unconstrained '''dSPM'''. <<BR>><<BR>> {{attachment:dspm.gif}}
 * Note that only the "Unconstrained" source orientation is available. In the previous tutorials, the source space was the cortical surface, and we were able to use the normals to this this surface to constrain the model. For a random grid of points, we cannot privilege one orientation more than another. Three orthogonal dipoles will be defined at each point of the grid.
 * Right-click on the volume dSPM sources for the Deviant average > '''Cortical activations'''. <<BR>><<BR>> {{attachment:treeSource.gif}}
 * The two menus '''Display on MRI (3D)''' and '''Display on MRI (MRI Viewer)''' were already introduced in the tutorial [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Display:_MRI_Viewer|Source estimation]]. You can use the sliders in the Surface tab to adjust the display.  The bilateral response in the auditory cortices is very clear starting from 60ms.<<BR>><<BR>> {{attachment:mri3d.gif||width="240px"}} {{attachment:mriViewer.gif||width="320px"}}

== Volume scouts ==
The regions of interest on the surface were introduced in the tutorial [[Tutorials/Scouts|Scouts]]. In a similar way, we can also create regions of interests from the volume sources. In this context, a scout is a subset of the the grid points used to estimate the sources. We cannot create them in the default atlas "User scouts", which is reserved to scouts created directly on the cortex surface.

 * Right-click on the volume dSPM sources for the Deviant average > '''Display on MRI (3D)'''.
 * Go to '''60ms''' and in the Surface tab, set the amplitude threshold to '''20%'''.
 * From the scout tab, create a new volume atlas: menu Atlas > New atlas > '''Volume scouts'''. {{attachment:atlas_volume.gif}}
 *

Create a new volume atlas: menu Atlas > New atlas > Volume scouts. The create scouts by clicking on the MRI slices in a 3D view. To move the slices: right-click an move the mouse.

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