Using the anatomy templates

Author: Francois Tadel

Brainstorm orients most of its database organization and processing stream for handling anatomical information together with the MEG/EEG recordings. The introduction tutorials start with the import of the T1 MRI of the subject, and this anatomy seems mandatory everywhere. These choices were made because the primary focus of Brainstorm was to estimate brain sources from MEG/EEG, which ideally requires an accurate spatial modelling of the head.

If you don't have access to anatomical images of your subjects or if you are not interested in source reconstruction, Brainstorm will still require that you explicitly define an anatomy; in those case you would use an anatomy template. In the case of group analysis at the source level, you would also use a template on which you would project of the individual results.

Several templates are available, with a large preference for using the MNI ICBM152 package distributed with Brainstorm because it provides the highest level of compatibility between different features within Brainstorm and with other software environments. You might be interested in using another one if you are working with different age ranges, or if you need to obtain results in a specific space. This tutorial provides references to the various templates available in Brainstorm.


An anatomy template is a set of anatomical files (MRI, surfaces, parcellations) representing a brain atlas. As the reference anatomy, we recommend using the ICBM125 2009c Nonlinear Asymmetric, distributed by default with Brainstorm, but other options are described below. An anatomy template can be used for various purposes:

When using an anatomy template as a substitution for the subject anatomy, you have to be careful with the spatial distortions it creates. As the reference anatomy has a different shape and cortical folding from your subject, with sometimes important differences in head size, it is preferable to follow these guidelines:

Subject configuration

Using the default anatomy

When creating a new subject, select the option "Yes, use protocol's default anatomy". This causes the contents of the subject anatomy folder to be replaced with the text Default anatomy. When a Brainstorm process or display function requests the default MRI or surfaces for this subject, the files from the Default anatomy are returned.

By default, all new protocols use as their default anatomy the simplified version of the ICBM152 MNI template distributed with Brainstorm (brainstorm3/defaults/anatomy/ICBM152). When creating the protocol, Brainstorm makes a copy of the ICBM152 anatomy, processed with FreeSurfer 6, and sets it as the default for the protocol. This template brain is used as a substitute for the subjects without an individual MRI, or as the common brain for group analysis.


Modify the default 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.

Changing the default anatomy

Other sets of MRI+surfaces are available to replace the ICBM152/FreeSurfer 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/CAT12 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.

MNI parcellations

It is possible to import anatomical parcellations of the brain defined in MNI space into any subject anatomy for which the MNI normalization was computed, or into any MNI anatomy template. Each parcellation is a volume of integers where each value represents an anatomical label, and registered to an MNI space. A non-linear deformation field can be applied to an MNI parcellation in order to create a volume parcellation in subject space. The anatomical regions defined in these files can be used as volume scouts, for reference in the MRI viewer, or for labelling SEEG contacts.

Right-click on the anatomy folder > Add MNI parcellation. There are some MNI parcellations available for download directly from the Brainstorm interface:

You can find detailed descriptions of these MNI parcellations, and link to many other atlases here:



Tutorials/DefaultAnatomy (last edited 2021-08-30 14:21:31 by FrancoisTadel)