= 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>><<BR>>  {{attachment:gridOptions.gif}}

 1. When the option "'''Generate from cortex surface'''" is selected, a grid that samples the head model in an adaptive way (denser at the surface, sparse at the center of the brain). This grid is created with following algorithm:
  * Start with a version of the brain envelope that has a given number of vertices (option '''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 on the downsampled layer
  * For each combination of parameters, you can see total number of vertices in the source grid at the bottom of the option window.
  * Click on '''Preview''' to see the grid of dipoles.<<BR>><<BR>> {{attachment:grid.gif|grid.jpg}}
 1. Alternatively, if you already have your grid of sources, you can import it directly from a file or from a Matlab variable
 1. Leave all the intial options, and click on Ok. A new head model is available in the condition Right: <<BR>><<BR>> {{attachment:treeHeadmodel.gif}}

== Compute sources for this grid ==
 1. Make sure your new volume head model is selected (displayed in green).
 1. Right-click on Subject01 / Right / ERF > Compute sources. Select '''Expert mode'''. Leave all the default options. Run.<<BR>><<BR>> {{attachment:wmne.gif}} {{attachment:wmneOptions.gif}}
 1. 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.
 1. Click on Ok. A new source file appears in the database.<<BR>><<BR>> {{attachment:treeSource.gif}}
 1. The only visualization modes available for this file are MRI views (3D orthogonal slices, or MRI Viewer).<<BR>><<BR>> {{attachment:mri3d.gif||height="244px",width="240px"}} {{attachment:mriViewer.gif||height="303px",width="320px"}}

== Volume scouts [TODO] ==
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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