DBA tutorial: Compute sources in deep cerebral structures

Authors: Jean-Eudes Le Douget, Francois Tadel, Denis Schwartz

This tutorial explains step-by-step how to use the DBA (Deep Brain Activity) functionality, useful to assess subcortical source localization.

Warnings: (added in April 2021)

  1. The mixed head models introduced in this tutorial are complicated to handle in terms of data structures, they produce values of different types in the same files, and have shown to cause many interpretation and computation errors among Brainstorm users. For general studies, we recommend using simpler source spaces: surface or volume.

  2. Mixed head models are mostly indicated for individual subject analysis, and not suitable for group analysis when using individual anatomy for all the subjects. We do not have any accurate solution for projecting the individual mixed source space to the template space. use volume head models instead. See tutorials: Volume source estimation, Subjects coregistration.

Import database

This tutorial is based on resting-state recordings for 7 subjects with two conditions: eyes open (YO), eyes closed (YF). We have recorded 20 runs of 15 seconds for each subject and each condition.

The goal is to compute the contrast between the two conditions in the alpha band. The data has already been filtered in the alpha frequency band (7-13Hz) and the default anatomy is used for all the subjects.

Select deep structures

The first step consists in creating the surface file that includes the cortex and the deep structures that we want to include in the model. Here, in the default anatomy:

Location and orientation constraints

Two types of constraints can be applied to each anatomical region in the atlas "Source model":

Based on the anatomical observations reported for each subcortical region in the reference articles (next section), the preferred combination of constraints is described below. The reference articles also estimate the number of averaged trials needed to detect responses in some regions.

Source estimation

Head model

Inverse model

Compute statistics

We will now design a statistical analysis to assess the eyes-open and eyes-closed contrast. As a reminder, the recordings available in the database have already been filtered in the alpha frequency band (7-13Hz). As a measure of the global of the activity in this frequency band, we will average all the time samples in each block of 15s. Note that this is not the recommended procedure anymore: it would have been better to simply compute a PSD from the sources estimated for the continuous file link, but this option was not available at the time this tutorial was written.

Volume scouts

Some subcortical structures are modeled as volume source structures (for instance here, the thalamus and the amygdala). It is not possible to display scouts time series for these structures from the "Source model" or "Structures" atlases. It is necessary to create a new atlas, specific to volume scouts. Volume scouts are described in the tutorial Volume source estimation. The only difference here is that you will be able to create them from the grid of points you see in the 3D figures (instead of the MRI slices).


Attal Y, Bhattacharjee M, Yelnik J, Cottereau B, Lefèvre J, Okada Y, Bardinet E, Chupin M, Baillet S (2009)
Modelling and detecting deep brain activity with MEG and EEG
IRBM, 30(3):133-138

Attal Y, Schwartz D (2013)
Assessment of Subcortical Source Localization Using Deep Brain Activity Imaging Model with Minimum Norm Operators: A MEG Study
PLOS ONE, 8(3):e59856

Dumas T, Dubal S, Attal Y, Chupin M, Jouvent R (2013)
MEG Evidence for Dynamic Amygdala Modulations by Gaze and Facial Emotions
PLOS ONE, 8(9): e74145

Additional documentation

Tutorials/DeepAtlas (last edited 2023-05-16 20:33:59 by ?MarcLalancette)