On Wed, Feb 20, 2008 at 10:46 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
On Wed, 20 Feb 2008, Mishkin Derakhshan wrote:
Hi,
- When using mris_convert lh.white lh.white.ascii, what co-oridnate
system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume?
These are "surface RAS" or "tkregister RAS". There is a power point presentation on coord systems on the wiki.
So according to the overview on https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems if I wanted to go from the SurfaceRAS (ie. what the lh.white.ascii is in) back to the coord system of my original volume, i would transform my object with the matrix M = inv(xform3)*inv(xform2)*inv(xform1) ? The diagram leads me to believe this is the same as M = inv(4)*inv(1) ?
The text also says the SurfaceRasFromVoxel matrix is: [ 3x3 part (t1 - c_r)] [ same as (t2 - c_a)] [ xform0 (t3 - c_s)] [ 0 1 ]
So the inverse of that would be what I'm looking for as well right? In that case, what is xform0? Just my directional cosines of the original image? Would t1,t2,t3 =0 then?
thanks for the help, mishkin
- I am making the assumption that the lh.white and the lh.pial will
always have the same number of indices and polygons. Can I also make the assumption that the order in which they are printed using mris_convert will be the same. ie. Will the vertex on line 54 of lh.white.ascii correspond to the same vertex on line 54 of lh.pial.ascii?
Yes.
doug
thanks, mishkin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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