Hello @claudiarodgadea ,
It is possible to use Brainstorm without the GUI, this is by generating a Matlab script, and execute it. Details to do so are described in this tutorial:
The script import_mri() only does that, to import a MRI volume into the Brainstorm DB, the process that you are looking is process_segment_cat12.m
function varargout = process_segment_cat12( varargin )
% PROCESS_SEGMENT_CAT12: Run the segmentation of a T1 MRI with SPM12/CAT12.
%
% USAGE: OutputFiles = process_segment_cat12('Run', sProcess, sInputs)
% [isOk, errMsg] = process_segment_cat12('Compute', iSubject, iAnatomy=[default], nVertices, isSphReg, isExtraMaps, isInteractive)
% process_segment_cat12('ComputeInteractive', iSubject, iAnatomy)
% @=============================================================================
% 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
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
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The process process_segment_cat12.m is called in these two examples:
In addition, check this other forum post:
Dear all,
Is there any way to 'batch' run CAT12 segmentation?
After add all T1 images to subjects, The CAT12 segmentation is disabled in pipeline tab, and only run one by one in the anatomy tab.