Can't export cortex (to gifti) and electrode locations in the same space

Francois · July 10, 2018, 9:48am

Hello,

All the 3D positions are saved in the Brainstorm database in the same coordinate system (SCS), vertices in the surface file and SEEG contact positions:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface
https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#On_the_hard_drive

If you export to external file formats (eg. gifti), there are additional spatial transformations that might be applied. You can follow step by step the transformations applied for a specific file format in the corresponding export function. Example:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_tess_gii.m#L47


% Load surface

if ischar(TessMat)

TessFile = TessMat;

TessMat = in_tess_bst(TessMat);

else

TessFile = [];

end



% ===== CONVERT TO MNI COORDINATES =====

% For export to SPM

if isSPM && ~isempty(TessFile)

% Get subject

sSubject = bst_get('SurfaceFile', TessFile);

% Get MRI file

MriFile = sSubject.Anatomy(1).FileName;

% Load the MRI

sMri = in_mri_bst(MriFile);

% Get transformation

if ~isfield(sMri, 'NCS') || ~isfield(sMri.NCS, 'R') || isempty(sMri.NCS.R)

    sMri.NCS.R = [1 0 0; 0 1 0; 0 0 1];

    sMri.NCS.T = -size(sMri.Cube)'./2;

Cheers
Francois