Doubt about MRI transformation at importing anatomy, and source modeling

Raymundo.Cassani · April 23, 2025, 1:03pm

Just to add more details on @SBeumer answer:

There are two transformations:

vox2ras, this transformation that can be included in the MRI data (for MGH or NIfTI formats), for transforming from Voxel (integer units) to Right-Anterior-Superior (RAS) orientation (millimeters).
tReorient: this is not explicitly included in the MRI data, but computed from the vox2ras. This second transformation is used to reorient the Voxel volume into the Brainstorm expected orientation. The idea with this is to have a MRI in voxels always oriented in the same way, regardless of the MRI device voxel orientation.

You can check the details in cs_nii2bst.m:

toolbox/anatomy/cs_nii2bst.m

bcf32d759

function [sMri, vox2ras, tReorient] = cs_nii2bst(sMri, vox2ras, isApply)
% CS_NII2BST: Converts a vox2ras transformation matrix from NIfTI format to Brainstorm format.
%
% USAGE:  [sMri, vox2ras, tReorient] = cs_nii2bst(sMri, vox2ras, isApply=[ask])

% @=============================================================================
% 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
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%

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