I think tksurfer reports the coords of the white surface

roberto toro wrote:

On 3/30/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:

...

What do you mean by the "actual 3d coordiantes in the mesh"? The RAS coord is the MNI305 coord. You can have tksurfer display it with View->Information->VertexMNITal. In this case it will be the same as the RAS. The Talairach coord is the MNI coord adjusted with Mathew Brett's algorithm, which is more than just a translation.

doug

Hi Doug,

Thanks for the clarification.

If you load fsaverage in tksurfer and click in a vertex, the interface will display the RAS and talairach coordinates, but you can read a different set of coordinates in the terminal window (X11). When I read fsaverage lh.pial directly with C code, the coordinates of the vertices are these coordinates that tksurfer displays in the terminal window., that's why I call them the "actual 3d coordinates in the mesh". tksurfer has to be using a transformation to convert the actual coordinates into the RAS, MNI or talairach coordinates displayed in the interface.

this is an example of tksurfer display for vertex 98832:

% surfer: dmin=0.2498, vno=98832, x=50.3003, y=14.1151, z=-32.7580 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 98832 marked (curv=0.000000, stat=0.000000) x = (50.3, 14.1, -32.8), n = (0.4, 0.9, -0.2). %

The MNI Talairach coordinates for the same vertex are (48.08 11.30 -31.69)

So, I would like to know which is the transformation matrix used to go from the actual to the MNI coordinates.

thanks in advance! roberto

...

On Fri, 30 Mar 2007, roberto toro wrote:

...

Hi,

I'm trying to figure out how to go from a coordinate in mni305 space to a vertex index in fsaverage. In the README file that comes with fsaverage it's stated that surface coordinates are in talairach space, so they align with the MNI305 volume (and the talairach.xfm is the identity). But when I select a vertex in fsaverage (using tksurfer) I have three different coordinates. For example, vertex 62176 gives

1. the actual 3d coordinate of the vertex in the mesh

-2.4876, -5.1338, 10.0494 2. the RAS coordinate -1.97, -4.48, 10.51 3. the Talairach coordinate (which I suppose are in fact MNI305 coordinates..) -1.95, -3.85, 9.87

this doesn't seem to be just a translation because when I compare actual 3d and talairach, the difference between the x coord (for example) of different vertices is not the same...

how does tksurfer convert to talairach coordinates?

thanks in advance!

roberto _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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