Conversion of coordinate system from SCS to world coordinate when exporting the mesh

Francois · March 18, 2022, 10:37am

Did you start the segmentation with ROAST from Brainstorm?
If you overlay the FEM mesh with the anatomy in a 3D figure in Brainstorm: does it look correctly aligned?

I'm still a bit confused by the way the coordinates of the ROAST results are handled, as it goes through iso2mesh as well... See the code:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_fem_mesh.m#L851


      
          % ===== VERIFY FIDUCIALS IN T1 MRI =====
          % If the SCS transformation is not defined: compute MNI transformation to get a default one
          if isempty(sMriT1) || ~isfield(sMriT1, 'SCS') || ~isfield(sMriT1.SCS, 'NAS') || ~isfield(sMriT1.SCS, 'LPA') || ~isfield(sMriT1.SCS, 'RPA') || (length(sMriT1.SCS.NAS)~=3) || (length(sMriT1.SCS.LPA)~=3) || (length(sMriT1.SCS.RPA)~=3) || ~isfield(sMriT1.SCS, 'R') || isempty(sMriT1.SCS.R) || ~isfield(sMriT1.SCS, 'T') || isempty(sMriT1.SCS.T)
              % Issue warning
              bst_report('Warning', 'process_fem_mesh', [], 'Missing NAS/LPA/RPA: Computing the MNI transformation to get default positions.');
              % Compute MNI normalization
              [sMriT1, errNorm] = bst_normalize_mni(sMriT1);
              % Handle errors
              if ~isempty(errNorm)
                  errMsg = [errMsg, 'Error trying to compute the MNI transformation: ' 10 errNorm 10 'Set the NAS/LPA/RPA fiducials manually.'];
                  return;
              end
          end            
          % === SAVE T1 MRI AS NII ===
          bst_progress('setimage', 'plugins/roast_logo.gif');
          bst_progress('text', 'Exporting MRI...');
          % Create temporary folder for fieldtrip segmentation files
          TmpDir = bst_get('BrainstormTmpDir', 0, 'roast');
          % Save MRI in .nii format
          subjid = strrep(sSubject.Name, '@', '');
          T1Nii = bst_fullfile(TmpDir, [subjid 'T1.nii']);

But if it looks good within Brainstorm, then this is taken care of correctly by Brainstorm and you should not have to worry about the fact that there are many intermediates.

we multiplied the vertices with 1000 to get millimeters to view in 3D Slicer

All the coordinates in Brainstorm are saved in SCS coordinates.
If you are using surfaces files that you found in the Brainstorm database, they are in SCS coordinates.
In order to use then somewhere else, you need to convert them to "world" or "mni" coordinates.

We exported the mesh vtk file after transforming the msh using gmsh to vtk

I have no expertise to comment on this part.

Good luck!