Tutorial 3: Display the anatomy

Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet

Anatomy folder

The anatomy of the subject "Subject01" should now contain all the files that Brainstorm could import from the FreeSurfer segmentation results:

Default surfaces

MRI Viewer

Right-click on the MRI to get the list of the available display menus:

Open the MRI Viewer. This interface was already introduced in the previous tutorial. It corresponds to the default display menu if you double-click on the MRI from the database explorer. Description of the window:

MRI contact sheets

You can get collections of slices in any direction (axial, coronal or sagittal) with the popup menus in the database explorer or the MRI Viewer figure.

MRI in 3D

Right-click on the MRI file in the database explorer > Display > 3D orthogonal slices.


To display a surface you can either double-click on it or right-click > Display. The tab "Surface" contains buttons and sliders to control the display of the surfaces.

Get coordinates

Sub-cortical regions

The standard FreeSurfer segmentation pipeline generates a volume atlas of 40 subcortical regions. Brainstorm reads these volume labels and tesselates some of these regions, then groups all the meshes in a large surface file where the regions are identified in an atlas called "Structures". It identifies: 8 bilateral structures (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus, cerebellum) and 1 central structure (brainstem).

These structures can be useful for advanced source modeling, but will not be used in the introduction tutorials. Please refer to the advanced tutorials for more information.

With the button [Struct] at the bottom of the Surface tab, you can see the structures separately. For more information, see the tutorial Deep cerebral structures.

Registration MRI/surfaces

The MRI and the surfaces are represented using the different coordinate systems and could be misregistered for various reasons. If you are using the automated segmentation pipeline from FreeSurfer or BrainSuite you should never have any problem, but if something goes wrong or in the case of more manual import procedures it is always good to check that the MRI and the surfaces are correctly aligned.


Interaction with the file system

For most manipulations, it is not necessary to know exactly what is going on at the level of the file system, in the Brainstorm database directory. However, many things are not accessible from the Brainstorm interface, you may sometimes find it useful to manipulate some piece of data directly from the Matlab command window.

Where are the files ?

Right-click on a surface file: many menus can lead you to the files and their contents.

What are all these other files ?


On the hard drive: MRI

Right-click on the MRI > File > View file contents:

Structure of the MRI files: subjectimage_*.mat

Useful functions


On the hard drive: Surface

Right-click on any cortex surface > File > View file contents:

Structure of the surface files: tess_*.mat

Useful functions

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Tutorials/ExploreAnatomy (last edited 2017-08-19 09:58:08 by FrancoisTadel)