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| = Import Database = = Select deep structures = |
= Compute sources in deep cerebral structures : DBA tutorial = 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. [[attachment:LoadProtocol]] The following steps detail a method to compute the Eyes-Open vs Eyes-Closed contrast in the alpha band. Note that the runs 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 wa 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 subatla * 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 as "Deep brain" [[attachment:SelectStructures]] [[attachment:MergeSurfaces]] [[attachment:RenameCtx]] [[attachment:SourceModelOptions]] [[attachment:SetModelingOptions]] == Compute source activity == Then, compute a headmodel for each subject as "Custom Head Model" ; it is advised to run it as batch from the pipeline editor. [[attachment:HeadModelBatch]] [[attachment:HeadModelOptions]] At this stage, it is now possible to compute sources. [[attachment:ComputeSources]] [[attachment:SourceOptions]] [[attachment:SourceOptions2]] == Visualize activity == == Compute statistics == |
Compute sources in deep cerebral structures : DBA tutorial
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 runs 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 wa 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 subatla
- 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 as "Deep brain"
SelectStructures MergeSurfaces RenameCtx SourceModelOptions SetModelingOptions
Compute source activity
Then, compute a headmodel for each subject as "Custom Head 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
Visualize activity