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.
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 TtestOptionsThe stat file can then be visualized and the values corresponding to subcortical structures are also appearing
VisuStatIt 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
VolumeFirstPointClick 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 RightThalRename 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