Coordinates in brainstorm

Francois · January 25, 2022, 9:09am

Unfortunately, I won't be able to help you much out of Brainstorm.
For exporting the SEEG coordinates, I guess you have only one possibility, which is to convert them to the scanner-based coordinate of the input file:
cs_convert(sMRI, 'scs', 'world', xyz)

I don't know how to guide you from there on. If you want details on how this transformation is read and stored in Brainstorm, see function in_mri_mgh.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_mri_mgh.m

function [sMri, vox2ras] = in_mri_mgh(MriFile, isApplyBst, isApplyVox2ras)
% IN_MRI_MGH: Read a structural MGH MRI (or gzipped MGZ).
%
% USAGE:  [sMri, vox2ras] = in_mri_mgh(MriFile, isApplyBst=[ask], isApplyVox2ras=[ask]);
%
% INPUT:
%    - MriFile    : full path to a MRI file, WITH EXTENSION
%    - isApplyBst : If 1, apply best orientation found to match Brainstorm convention
%                   considering that the volume is aligned as the standard T1.mgz in the 
%                   FreeSurfer output folder.
%    - isApplyVox2ras : Apply additional transformation to the volume
% OUTPUT:
%    - sMri    : Standard brainstorm structure for MRI volumes
%    - vox2ras : [4x4] transformation matrix: voxels to RAS coordinates
%
% FORMAT: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm

This file has been truncated. show original

There is an export function to FreeSurfer surface format, however I'm not sure how correct this is, I don't think it has been used much. Maybe the transformation and/or its label are wrong. But it might inspire you for more tests:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_tess.m#L82

    
      
              % Convert to BrainVISA MRI coordinates

              if ~isempty(sMri)

                  mriSize = size(sMri.Cube(:,:,:,1)) .* sMri.Voxsize(:)' ./ 1000;

                  TessMat.Vertices = bst_bsxfun(@minus, mriSize, TessMat.Vertices);

              end

              % Export file

              out_tess_gii(TessMat, OutputFile, 0);

          case 'FS'

              % Swap faces

              TessMat.Faces = TessMat.Faces(:,[2 1 3]);

              % MRI => FreeSurfer RAS coord

              if ~isempty(sMri)

                  % TessMat.Vertices = bst_bsxfun(@minus, TessMat.Vertices, [128 129 128] / 1000);

                  TessMat.Vertices = bst_bsxfun(@minus, TessMat.Vertices, (size(sMri.Cube(:,:,:,1))/2 + [0 1 0]) .* sMri.Voxsize / 1000);

              end

              % Export file

              out_tess_fs(TessMat, OutputFile);

          case 'OFF'

              out_tess_off(TessMat, OutputFile);

          case 'TRI'

              out_tess_tri(TessMat, OutputFile);