Hi,
1. 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?
2. 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?
thanks, mishkin
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.
- 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
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Sorry, look at the power point slides just above that section, the ones here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFil...
doug
Mishkin Derakhshan wrote:
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Mishkin Derakhshan