Finding SCS translation and rotation matrix (MRI (voxel) to SCS)

mohammadrezarezaeid · July 7, 2022, 12:54am

Hello,

I was wondering how you find the SCS translation and rotation matrix (SCS.R and SCS.T). Could you please explain (or put the link to the code)?

Thanks,

Mohammadreza

Francois · July 8, 2022, 10:37am

The SCS transformation is computed in function cs_compute.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/anatomy/cs_compute.m#L34

      
        
            %

            % For more information type "brainstorm license" at command prompt.

            % =============================================================================@

            %

            % Authors: Francois Tadel, 2008-2022

            

            Transf = [];

            

            switch lower(csname)

                % ===== MRI => SCS =====

                case 'scs'

                    % The necessary points are not defined

                    if isempty(sMri) || ~isfield(sMri, 'SCS') || ~isfield(sMri.SCS, 'NAS') || ~isfield(sMri.SCS, 'LPA') || ~isfield(sMri.SCS, 'RPA') || (length(sMri.SCS.NAS)~=3) || (length(sMri.SCS.LPA)~=3) || (length(sMri.SCS.RPA)~=3)

                        disp('BST> Cannot compute MRI=>SCS transformation: Missing fiducial points.');

                        return;

                    end

                    % Get coordinates

                    NAS = double(sMri.SCS.NAS(:));

                    LPA = double(sMri.SCS.LPA(:));

                    RPA = double(sMri.SCS.RPA(:));

                    % Origin: Mid point between LPA and RPA

Then saved in the reference MRI:
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_MRI