Export surfaces from BS is not in the same space as the FS subject

Boris_Rauchmann · March 29, 2019, 2:58pm

Dear Francois,

we are using the BS export function of surface source maps to SPM12 for further statistical analysis in PALM. When I compared the export cortex .gii file and the original fs pial files they are apparently not in the same space. Does BS do any registration to the fs surface files when generating the head model for source estimation?

Is there a way to directly export surface source maps in standard space?

See the mismatch in the attached picture.

Thanks,
Boris

Francois · April 1, 2019, 5:24pm

There are multiple transformations applied to the surfaces when reading or saving them.
The sequence of transformations depends on the file format. When exporting surfaces as .gii, it assumes it is for exporting files in the same format and coordinate system as BrainVISA.

If you want to export back to FreeSurfer a surface initially coming from FreeSurfer (loaded with the menu "Import anatomy folder"), you should use the file format "FreeSurfer" when exporting the surface from the database explorer.

The corresponding code, in case you want to fix this manually:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_tess.m#L41




% ===== PARSE INPUTS =====

if (nargin < 4)

sMri = [];

end



% ===== LOAD SURFACE =====

% Load Brainstorm file

TessMat = in_tess_bst(BstFile);

% Convert back to MRI coordinates

if ~isempty(sMri)

TessMat.Vertices = cs_convert(sMri, 'scs', 'mri', TessMat.Vertices);

else

disp('BST> Warning: MRI is missing, cannot convert surface to Brainstorm coordinate system.');

end





% ===== SAVE SURFACE =====

[fPath, fBase, fExt] = bst_fileparts(OutputFile);

% Show progress bar

bst_progress('start', 'Export surface', ['Export surface to file "' [fBase, fExt] '"...']);

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_tess.m#L97


        FileFormat = 'FS';

end

end

% If format was not detected

if strcmpi(FileFormat, 'ALL')

bst_error(['File format could not be detected automatically.' 10 'Please try again with a specific file format.'], 'Import surface', 0);

return;

end





%% ===== READ SURFACE =====

% Switch between different import functions 

switch (FileFormat)

case 'BST'

    TessMat = in_tess_bst(TessFile);

    isConvertScs = 0;

case 'DFS'

    TessMat = in_tess_dfs(TessFile);

    % Add a one voxel shift in all the directions to the surface (ADD FT: 12-Jan-2016)

    if ~isempty(sMri)

        TessMat.Vertices = bst_bsxfun(@plus, TessMat.Vertices, sMri.Voxsize / 1000);