Using the anatomy templates

Author: Francois Tadel

Changing the default anatomy

When you create a new protocol, the program makes a copy of the ICBM152 or Colin27 anatomy and sets it as the default for the protocol. It means that you will be able to use this template brain as a substitute for the subjects without an individual MRI, or as the common brain for group analysis.

Other sets of MRI+surfaces are available to replace the Colin27 anatomy. Right-click on (Default anatomy) > Use template. If a package is not currently available on your system, it will be downloaded from the Brainstorm website and saved in $HOME/.brainstorm/templates.

If you click on any of the download options, it downloads it into your $HOME/.brainstorm/templates folder, then the list of files in the (default anatomy) folder is replaced with the new template.

Group analysis

When performing a group analysis with multiple subjects for which you have the individual MRI scans, you need to project the sources estimated on each subject on a common template, as explained in this tutorial: Group analysis.

For accurate registration between different brains (from a subject to a template or between subjects), you need to use a template that was generated using the same program as the one you used for running the segmentation of all the subjects of your studies.

You can use either BrainSuite or FreeSurfer for processing the MRIs or your subjects, but you need to use a template that matches this choice in order to use the accurate registration methods.

FreeSurfer templates

Available options:

• Colin27: Average of 27 scans of the same head, processed with FreeSurfer 5.3: more information

• ICBM152: Non-linear average of 152 subjects, processed with FreeSurfer 5.3: more information

• FSAverage: Average of 40 subjects using a spherical averaging described in (Fischl et al. 1999).
  It is the default FreeSurfer brain: please register here if you are using it.
  More images: http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#FSAverage_template

They all include the following information:

• T1 MRI volume
• Cortex surface: high-resolution (~300.000 vertices) and low-resolution (15.000 vertices)
• Head surface: based on the head used for FSAverage in the MNE software

• FreeSurfer spherical registration of each hemisphere, with which we can co-register the individual brains processed with FreeSurfer with the selected default anatomy

• FreeSurfer surface-based atlases: Desikan-Killiany, Destrieux, Brodmann, Mindboggle
  (plus Yeo2011 and PALS for FSAverage only)

For more information on the interactions between FreeSurfer and Brainstorm: read this tutorial.

BrainSuite templates

Available options:

BrainVISA templates

Note that the BrainVISA-based templates do not allow any accurate registration procedure.

• Colin27_2012: Previous version of the default anatomy distributed with Brainstorm.

• Infant7w: 7-week infant brain with the antomical atlas presented in (Kabdebon et al. 2014).

• Oreilly_1y: 1 year old infant brain with Tzourio-Mazoyer surface atlas (Li et al. 2015, Shi et al. 2011): http://neuroimage.usc.edu/forums/showthread.php?2123-Atlas-for-1-year-old-babies

Modify the default MRI fiducials

The fiducial points (Nasion, LPA, RPA) used in your recordings might not be the same as the ones used in the anatomy templates in Brainstorm (Colin27, ICBM152, FSAverage). By default, the LPA/RPA points are defined at the junction between the tragus and the helix, as represented with the red dot in the Coordinates systems page.

If you want to use an anatomy template but you are using a different convention when digitizing the position of these points, you have to modify the default positions of the template with the MRI Viewer.

• Go to the anatomy view

• In (default anatomy), right-click on the MRI > Edit MRI

• Modify the position of the fiducial points to match your own convention
• Click on [Save], it will update the surfaces to match the new coordinate system