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 anatomy (previously Colin27) 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 ICBM152 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 templates folder, then the list of files in the (default anatomy) folder is replaced with the new template.

If the automatic download doesn't work, you can download the templates manually from the Download page and copy the .zip files directly in the folder $HOME/.brainstorm/templates.

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:

They all include the following information:

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

BrainSuite templates

Available options:

Warning: If you are using BrainSuiteAtlas1 for BrainSuite processing, then you should use Colin27_BrainSuite_2016 or ICBM152_BrainSuite_2016 as the default anatomy. If you are using the BCI-DNI_brain_atlas, then you should use BCI-DNI_BrainSuite_2016 as the template in BrainStorm.

They all include the following information:

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

BrainVISA templates

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

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. 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.

Tutorials/DefaultAnatomy (last edited 2017-07-26 20:04:43 by ?AnandJoshi)