Dear Brainstorm Developer, Users
I want to do deep brain + cortex source modeling for my project and that works very well in the GUI, Although I need to automatize the process and loop over my subjects in a script.
new atlas "Source model options "
set modeling options to "Deep brain "
Any Idea about corresponding functions?
1 Like
Hi @etohidi ,
Apologies for the delay in answering, we just 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:
function tutorial_dba(zip_file, reports_dir)
% TUTORIAL_DBA: script that runs the Brainstorm deep brain activity (DBA) tutorial.
% https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas
%
% INPUTS:
% - zip_file : Full path to the TutorialDba.zip file
% - reports_dir : Directory where to save the execution report (instead of displaying it)
%
% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
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Such script shows how to perform the steps you asked. Let us know if you require further information. Best, Raymundo
2 Likes
Dear @Raymundo.Cassani I really appreciate you providing this, I have adapted my script, Yesterday I was trying to manually modify the structure according to https://neuroimage.usc.edu/forums/t/scripting-deepatlas-select-deep-structures/9661/2 of the merged surfaces and saving it back to the brainstorm, but somehow brainstorm didn't accept the new modified Atlas, But this totally works!
Best