World Coordinates using Freesurfer

BarryLiu · December 10, 2021, 2:46pm

Hi, from the tutorial here, it says

World coordinates
Coordinates system used in the original MRI file, that was loaded as the reference MRI for a subject.

So if I used the Freesurfer result, I saw it automatically imported T1.mgz, we know that this file is in Surface RAS coordinates, which means the center is (almost) in the center of the (256 x 256 x 256 1mm) MRI. In this case, the world coordinate equals the Surface RAS(also called tkras)?

Francois · December 13, 2021, 11:20am

The vox2ras transformation is loaded from the .mgz files here:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_mri_mgh.m#L94


if (hdr.ras_good_flag)

    Voxsize = fread(fid, 3, 'float32')' ;

    hdr.Mdc     = fread(fid, 9, 'float32') ;

    hdr.Mdc     = reshape(hdr.Mdc,[3 3]);

    hdr.Pxyz_c  = fread(fid, 3, 'float32') ;

    unused_space_size = unused_space_size - (3*4 + 4*3*4) ; % space for ras transform

    % Assemble vox2ras matrix

    D = diag(Voxsize);

    Pcrs_c = [hdr.ndim1/2, hdr.ndim2/2, hdr.ndim3/2]'; % Should this be kept?

    Pxyz_0 = hdr.Pxyz_c - hdr.Mdc * D * Pcrs_c;

    vox2ras = [hdr.Mdc * D, Pxyz_0;  ...

	           0 0 0 1];

else

    vox2ras = [];

end



% Position at the end of the header

fseek(fid, unused_space_size, 'cof') ;





%% ===== LOAD MRI VOLUME =====

When reading FreeSurfer .mgz files from the menu Import anatomy folder, a transformation is applied to the MRI (and the vox2ras matrix) to save the volume in a standard Brainstorm orientation:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_mri_mgh.m#L146




%% ===== TRANSFORM TO BRAINSTORM COORDINATES =====

% Ask user

if isempty(isApplyBst)

    isApplyBst = java_dialog('confirm', ['Apply the standard transformation FreeSurfer=>Brainstorm?' 10 10 ...

                                         'Answer "yes" if importing transformed volumes such as T1.mgz in the' 10 ...

                                         'FreeSurfer output folder, or other volumes in the same folder.' 10 10],  'MRI orientation');

end



% Apply transformation

if isApplyBst

    % Permute MRI dimensions

    Cube = permute(Cube, [2 3 1]);

    Voxsize = Voxsize([2 3 1]);

    % Rotation / Axis Y

    Cube = permute(Cube, [3 2 1]);

    Cube = bst_flip(Cube, 3);

    Voxsize = Voxsize([3 2 1]);

    % Flip / X

    Cube = bst_flip(Cube, 1);

I'm not sure how this translates into the FreeSurfer vocabulary. Since the surfaces are saved in a coordinate system that is very easy to relate to the MRI volume (without requiring the use of this vox2ras transformation), we never get back to the original FreeSurfer scanner-based coordinates.

If you doubt about the correspondence of coordinate systems, display the volume with the FreeSurfer tools and with the Brainstorm MRI viewer, and verify that you get the same coordinates for a few easy-to-identify voxels.

BarryLiu · December 13, 2021, 12:15pm

All right! Thank you so much!!!