Dear doug,

Thank you for your quick reply - Unfortunately this does not yet work. I have written a small matlab example to more clearly show my problem:

clear all; clc;

% I would like to load a surface with 
% [rh.pial.vertices,rh.pial.faces] = read_surf([surfdir 'rh.pial' ]);
% 
% rh.pial.vertices(59551,:) for example yields the vertex coordinates for
% vertex 59550: [34.2031  -24.7783   44.7629]

% when I open the image and the surface in freeview I can select this
% vertex and freeview tells me, that the voxel position in the image is [293 275 236]
% and the RAS is [44.19 -15.96 73.19]

% how can I calculate the voxel position or the RAS 
% based on the vertex coordinates I obtained with read_surf?

% This is what I tried so far:

%% example: Vertex 59550
RAS = [44.19 -15.96 73.19];
ImageVoxel = [293 275 236];
VertexCoordinate = [34.20 -24.78 44.76];

%% Image
originator = [  2.060349426269531e+02, ...
                2.073668823242188e+02, ...
                90.155899047851560, ...
                31551,...
                -7805];

sMatrix = [ 0.5    ,0      ,0      ,-1.025174713134766e+02; ...
            0      ,-0.5   ,0      ,1.213165588378906e+02; ...
            0      ,0      ,0.5    ,-44.577949523925780;
            0       ,0      ,0      ,1];

%% RAS2Vox
Ras2VoxTransf = inv(sMatrix); 
Ras2VoxResult = round(RAS * Ras2VoxTransf(1:3,1:3)+Ras2VoxTransf(1:3,4)');

% now Ras2VoxResult is equal to ImageVoxel :)
% now I only need a transform from VertexCoordinate to RAS ...


%% RasTkr2Vox
vox2rastkr = [-0.50000    0.00000    0.00000  112.50000; ...
   0.00000    0.00000    0.50000  -73.00000; ...
   0.00000   -0.50000    0.00000  112.50000; ... 
   0.00000    0.00000    0.00000    1.00000];

Ras2VoxTkrTransf = inv(vox2rastkr);
Ras2VoxTkrResult = round( ...
                    VertexCoordinate * Ras2VoxTkrTransf(1:3,1:3)+ ...
                    Ras2VoxTkrTransf(1:3,4)');
                
% This yields not the desired result - so, which Matrix do I have to use?


Thank you
Steffen


2011/2/9 Douglas N Greve <greve@nmr.mgh.harvard.edu>
The --vox2ras-tkr transform will take you to voxel space in the conformed coordinates (not the raw input). Is this good enough?
doug

Steffen Bollmann wrote:
Dear freesurfer experts,

I would like to display freesurfer surfaces in the voxelspace of the original subject image using matlab.

Which coordinate transformation do I have to apply to get the vertex-coordinates to the RAS space and finally to the original voxelspace of the subject? (i guess for RAS2Vox I can use the matrix I can obtain with mri_info ... but I cannot find a way from vertex-coordinates to RAS)

Thank you for any hint
Best Regards
Steffen Bollmann
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