Tutorial 2: Import the subject anatomy

Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet

Brainstorm orients most of its database organization and processing stream for handling anatomical information together with the MEG/EEG recordings, because its primary focus was to estimate brain sources from MEG/EEG, which ideally requires an accurate spatial modelling of the head and sensors.

If you don't have anatomical scans of your subjects or are not interested in any spatial display, various solution will be presented along the tutorials, starting from the last section of this page. Be patient and follow everything as instructed, you will get to the information you need.


The dataset we will use for the introduction tutorials is available online.

Create a new subject

The protocol is currently empty. You need to add a new subject before you can start importing data.

  1. Switch to the anatomy view (first button just above the database explorer).
  2. Right-click on the top folder TutorialIntroduction > New subject.
    Alternatively: Use the menu File > New subject.


  3. The window that opens lets you edit the subject name and settings. It offers again the same options for the default anatomy and channel file: you can redefine for one subject the default values set at the protocol level if you need to. See previous tutorial for help.


  4. Keep all the default settings and click on [Save].

Right-click doesn't work

If the right-click doesn't work anywhere in the Brainstorm interface and you cannot get to see the popup menus in the database explorer, try to connect a standard external mouse with two buttons. Some Apple pointing devices do not interact very well with Java/Matlab.

Alternatively, try to change the configuration of your trackpad in the system preferences.

Import the anatomy

For estimating the brain sources of the MEG/EEG signals, the anatomy of the subject must include at least three files: a T1-weighted MRI volume, the envelope of the cortex and the surface of the head.

Brainstorm cannot extract the cortex envelope from the MRI, you have to run this operation with an external program of your choice. The results of the MRI segmentation obtained with the following programs can be automatically imported: FreeSurfer, BrainSuite, BainVISA, CAT12, and CIVET. CAT is the only application fully interfaced with Brainstorm, and available for download as a Brainstorm plugin. However, FreeSurfer is more considered as a reference in this domain, therefore this is the solution we decided to demonstrate in these tutorials.

The anatomical information of this study was acquired with a 1.5T MRI scanner, the subject had a marker placed on the left cheek. The MRI volume was processed with FreeSurfer 7.1, the result of this automatic segmentation process is available in the downloaded folder sample_introduction/anatomy.

  1. Make sure that you are still in the anatomy view for your protocol.
  2. Right-click on the subject folder > Import anatomy folder:

    • Set the file format: FreeSurfer + Volume atlases

    • Select the folder: sample_introduction/anatomy

    • Click on [Open]
  3. Number of vertices of the cortex surface: 15000 (default value).
    This option defines the number of points that will be used to represent the cortex envelope. It will also be the number of electric dipoles we will use to model the activity of the brain. This default value of 15000 was chosen empirically as a good balance between the spatial accuracy of the models and the computation speed. More details later in the tutorials.


  4. The MRI views should be correct (axial/coronal/sagittal), you just need to make sure that the marker on the cheek is really on the left of the MRI. Then you can proceed with the fiducial selection.


Using the MRI Viewer

To help define these fiducial points, let's start with a brief description of the MRI Viewer:

Fiducial points

Brainstorm uses a few reference points defined in the MRI to align the different files:

Nasion (NAS)

Left ear (LPA)

Right ear (RPA)

Anterior commissure (AC)

Posterior commissure (PC)

Inter-hemispheric point (IH)

Type the coordinates


Graphic bugs

If you do not see the cortex surface through the head surface, or if you observe any other issue with the 3D display, there might be an issue with the OpenGL drivers. You may try the following options:

For Linux users with an integrated GPU and NVIDIA GPU, if you experience the troubles above, or the slow navigation in the 3D display (usually with 2 or more surfaces). Verify that you are using the NVIDIA GPU as primary GPU. More information depending on your distribution: Ubuntu, Debian and Arch Linux.

MNI normalization

For comparing results with the literature or with other imaging modalities, the normalized MNI coordinate system is often used. To be able to get "MNI coordinates" for individual brains, an extra step of normalization is required.

To compute a transformation between the individual MRI and the ICBM152 space, you have two available options, use the one of your choice:

Select the first option maff8: This method is embedded in Brainstorm and does not require the installation of SPM12. It is based on an affine co-registration with the MNI ICBM152 template from the SPM software, described in the following article: Ashburner J, Friston KJ, Unified segmentation, NeuroImage 2005.


Note that this normalization does not modify the anatomy, it just saves a transformation that enables the conversion between Brainstorm coordinates and MNI coordinates. After computing this transformation, you have access to one new line of information in the MRI Viewer.

This operation also sets automatically some anatomical points (AC, PC, IH) if not defined yet. After the computation, make sure they are correctly positioned. You can run this computation while importing the anatomy, when the MRI viewer is displayed for the first time, this will save you the trouble of marking the AC/PC/IH points manually.

MacOS troubleshooting

Error "mexmaci64 cannot be opened because the developer cannot be verified":


The head surface looks bad: You can try computing another one with different properties.

No individual anatomy: If you do not have access to an individual MR scan of the subject, or if its quality is too low to be processed with FreeSurfer, you have other options:

Other options for importing the FreeSurfer anatomical segmentation:

Feedback: Comments, bug reports, suggestions, questions
Email address (if you expect an answer):

Tutorials/ImportAnatomy (last edited 2022-06-10 10:31:57 by FrancoisTadel)