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 <gr...@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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>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
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>
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