For going from MNI to Talairach (or vice-versa) there are also the transforms that Lancaster derived -- these are citable because they are published.

See http://brainmap.org/icbm2tal/

which contains links to the relevant matlab scripts.

cheers, -MH

On Thu, 2012-05-03 at 12:54 -0400, Douglas N Greve wrote:

Here's how to convert from surface RAS to mni305

mni305ras = X*S*inv(K)*ras X = talairach.xfm S = scanner vox2ras (mri_info --vox2ras orig.mgz) K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) ras = surface ras

If you want to go from mni305 to approximate talairach, you can use this transform from Matthew Brett:

function outpoints = mni2tal(inpoints) % Converts coordinates from MNI brain to best guess % for equivalent Talairach coordinates % FORMAT outpoints = mni2tal(inpoints) % Where inpoints is N by 3 or 3 by N matrix of coordinates % (N being the number of points) % outpoints is the coordinate matrix with Talairach points % Matthew Brett 10/8/99

dimdim = find(size(inpoints) == 3); if isempty(dimdim) error('input must be a N by 3 or 3 by N matrix') end if dimdim == 2 inpoints = inpoints'; %' end

% Transformation matrices, different zooms above/below AC upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);

tmp = inpoints(3,:)<0; % 1 if below AC inpoints = [inpoints; ones(1, size(inpoints, 2))]; inpoints(:, tmp) = downT * inpoints(:, tmp); inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); outpoints = inpoints(1:3, :); if dimdim == 2 outpoints = outpoints'; %' end

On 05/02/2012 12:54 PM, Jordan Poppenk wrote:

...

Dear FreeSurfer experts,

How does one properly convert from surfaceRAS coords, as provided by fs_read_surf.m, to talairach coords? I have tried using freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with transform data from transforms/talairach.xfm, but the values returned often differ from those in tksurfer by as much as 20mm (and are clearly wrong). What I would like to do is match the coordinate system in tksurfer (which is clearly right). How does tksurfer do it?

Cheers, Jordan

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