Compute sources in deep cerebral structures : DBA tutorial

Authors: Jean-Eudes Le Douget, Denis Schwartz

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

Import database

To follow through the tutorial, the dataset can be downloaded *here*.

It contains MEG resting-state recordings of 7 subjects under 2 conditions, eyes-open (YO) and eyes-closed (YF). For each subject and under each condition, 20 runs of 15 seconds are included in the dataset.

The dataset is already in Brainstorm format and simply needs to be loaded via File > Load Protocol. LoadProtocol

The following steps detail a method to compute the Eyes-Open vs Eyes-Closed contrast in the alpha band.

Note that the data have already been filtered in the alpha frequency band (7-13Hz) and that for simplicity, default anatomy is used for all 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:

• Double-click on "aseg atlas" (which contains the subcortical structures)
• Select the amygdala, the thalamus and the hippocampus, and create a subatlas
• Merge the cortex with the atlas of selected structures ; rename the structure created in CortexDBA
• Create a new atlas "Source Model Atlas", and set modeling options to "Deep brain"

SelectStructures MergeSurfaces RenameCtx SourceModelOptions SetModelingOptions

Compute source activity

Then, compute a headmodel for each subject as "Custom Source Model" ; it is advised to run it as batch from the pipeline editor.

HeadModelBatch HeadModelOptions

At this stage, it is now possible to compute sources.

ComputeSources SourceOptions SourceOptions2

You can now visualize activity the same way as for usual headmodels.

VisuActivity

If the activity of the volume structures (thalamus and amygdala here) do not appear, try moving the Min size cursor to max and then back to 1.

Compute statistics

Now that the source calculations are done, we design a statistical analysis to assess the eyes-open and eyes-closed contrast.

• First, the alpha-power is time-averaged for each run
  AverageTime [[attachment:AverageTimeOptions3]]

• Then, the "Process2" tab is used : place the source power files of the eyes-closed condition in the "Files A" space and of the eyes-open condition in the "Files B" space.
  To gain time, it is possible to sort the functional data by conditions, place the subjects in "FilesA" and "FilesB" and use the filter to include only files that contain 'avg' (for time-averaged files)

• Run a Student's T-Test to compute a statistical contrast between the conditions
  Ttest TtestOptions

• The stat file can then be visualized and the values corresponding to subcortical structures are also appearing
  VisuStat

• It is also interesting to observe the difference of means between conditions. To compute this, instead of runnning a Student's T-Test, select the "Difference of means" option
  DiffOfMeans

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 volumic scouts. The steps are the following :

• First, create the volumic atlas
  VolumeScouts

• Second, to create a new scout :

  • Click on the "Create scout" cross, and click one point of the structure you want to include in the scout
    VolumeFirstPoint

  • Click on the "Increase scout size" as many times as necessary to include all the points of the volume, for example in the right thalamus
    IncreaseScoutSize RightThal

  • Rename the scout and set the correct region and the desired function
    RenameScout SetRegion SetFunction

  • Repeat this operation for all the volumic scouts you want to create

• Finally, you can display time series of your choice
  DisplayScoutsTS