Bruce,
Thanks. I'm approaching a solution, but not quite there yet.
I'm assuming you meant that I should use mris_convert (not
mri_convert) to create the ascii version of my surface file. I did
this as follows:
mris_convert rh.inflated rh.inflated.asc
However, the resulting ascii file does not contain RAS coordinates.
Rather, it contains x,y,z coordinates in a format I do not understand,
exemplified by this:
#!ascii version of rh.inflated
145185 290366
-32.980091 -124.283272 -37.115761 0
-33.141834 -124.183533 -37.142693 0
-33.435402 -123.985886 -37.259331 0
-32.554119 -124.488083 -37.194771 0
...etc...
I've been wondering what these coordinates are (I hope I"m not missing
something obvious here). These coordinates are not RAS nor voxel
coords. They are, however, shown in the tksurfer logs when I click on
points. That is, if I click on the 0th vertex in Tksurfer and then
SAVE that point, I see the following effects in the log (the x,y,z
coords below are the same as in the first row of the ascii
file shown above):
----------------------------
surfer: dmin=0.1721, vno=0, x=-32.9801, y=-124.2833, z=-37.1158
surfer: curv=-0.230000, fs=0.000000
surfer: val=0.000000, val2=0.000000
surfer: amp=0.000000, angle=0.000000 deg (0.000000)
surfer: vertex 0 marked (curv=-0.230000, stat=0.000000)
x = (-33.0, -124.3, -37.1), n = (-0.5, -0.9, -0.1).
writing coordinates to file
/home/alkim/freesurfer_alpha/subjects/E12410/tmp/edit.dat
vertex 0 coordinates:
ORIGINAL (11.5 -88.5 -8.5)
SPHERICAL (6.7 -90.2 -41.2): (114.5, -85.8)
----------------------------
So... could you either:
1) Tell me how to produce RAS coordinates in my ascii file or
2) Could you point me to an explanation of the coordinates that I am
seeing in my ascii file
Thanks very much,
Al
Department of Psychology
University of Washington, Box 351525
Seattle, WA. 98195, USA
E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395
On Mon, 4 Mar 2002, Bruce Fischl wrote:
> Hi Albert,
>
> you should be able to use spherical coordinates in order to compute
> approximate geodesic distances (the length of the arc along the great
> circle connecting two points will be an approximation of the geodesic
> distance on the gray/white boundary surface). The typical error for cortex
> is around 10-15%.
>
> I'm not clear what you want to do when you say "draw on the
> Freeurfer-reconstructed surface". There is a coordinate transform in the
> COR-.info file that should be able to take you from RAS coords to voxel
> ones, but there's really no need. If you have the RAS coordinates, you
> should be able to read out the vertex coordinates from the ascii version of
> the surface file (generating using mri_convert) and search through the
> vertex list to find the closest one to each of your points. You could also
> enter these into a label file, which has a simple ascii format, and load it
> to display your points.
>
> Does that help?
>
> Bruce
>
>
> On Mon, 4 Mar 2002, Albert Kim wrote:
>
> > Hi,
> >
> > I have a set of coordinates, indicating sites on a patient's cortical
> > surface (data from intraoperative cortical stimulation studies), which I
> > would like to draw on the Freeurfer-reconstructed surface. That is, I
> > would like the ability to relate my coordinates to locations (vertex
> > numbers??) on the reconstructed surface. [I have the coordinates of
> > these locations with respect to the scanner, and I can transform such
> > coordinates into coordinates within the COR-image space.]
> >
> > Note: I suppose one possiblity is to create a "fake" functional volume,
> > in which I light up the voxels that are closest to my surface locations,
> > and use the existing functional overlay mechanism. But if possible, I'd
> > like to do things more directly.
> >
> > If possible, I'd also like to know how to calculate distance along the
> > cortical surface between two points.
> >
> > Is there some function in the system that will accomplish these goals?
> > I'm assuming that there is some way to just tap into the existing overlay
> > functionality or the SEND and GOTO point utilities.
> >
> > Thanks,
> > Al Kim
> > Department of Psychology
> > University of Washington, Box 351525
> > Seattle, WA. 98195, USA
> > E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395
> >
> >
>
>
