[Scripting] DeepAtlas: Select_deep_structures

Discussions
, ,
1

Hello,
I want to make a script to create a mixed-head model as the DBA tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas#Select_deep_structures

I succeeded in generating "cortex_mixed" using the tess_downsize, tess_extract_struct, and tess_concatenate functions.
However, I having difficulty in these parts: "Create a new atlas Source model options" and Set the set modeling options to "Deep brain" for all the structures. It seems like panel_scout.m is managing it, but it is difficult to extract only those parts.
Do you have any suggestions for this problem?

Thank you so much,
Best,

Hyun Seok Kim

2

Hello,

I’m sorry, there is currently no easy solution for setting the modeling properties of the various regions from a script. You could try modifying the structure manually:

  • load the surface file: TessMat = in_tess_bst(TessFile)
  • modify the Region field of the scouts (2nd letter: S=Surface, V=Volume, D=dba - 3rd letter: C=Constrained, L=Loose, U=Unconstrained)
  • save the file back on the hard drive: bst_save(file_fullpath(TessFile), TessMat, ‘v7’)

Good luck with the script editing
Francois

3

In August 2024, we added the Matlab script to reproduce the DBA tutorial in commit 4855817

Update your Brainstorm instance and you will see the script tutorial_dba.m in the toolbox/scripts/ directory of Brainstorm. This is the file: