yes, but it's the original coordinates that matter, and the inflated or flattened ones are somewhat irrelevant.
Bruce On Thu, 7 Mar 2002, Albert Kim wrote: > > Hi Bruce, > > It seems to me that vertices in the surfer window are associated with at > least two coordinate descriptions. I include below info about the 0th > vertex on my rh.inflated surface, which is excerpted from my previous > email: > > A. surfer: dmin=0.0569, vno=0, x=-32.9801, y=-124.2833, z=-37.1158 > B. ORIGINAL (11.5 -88.5 -8.5) > > This vertex corresponds to voxel coords (116, 136, 39) > > I understand that the vertex coordinates in B above can be related easily > to the voxel coords. But I do not understand the coordinates in A. > And I'm trying to work with the A coordinates -- these are the coordinates > I get when I convert my ?h.inflated file into ascii format. > > Thanks, > Al > Department of Psychology > University of Washington, Box 351525 > Seattle, WA. 98195, USA > E-Mail: [EMAIL PROTECTED]; Tel: (206)543-2395 > > > On Thu, 7 Mar 2002, Bruce Fischl wrote: > > > Hi Al, > > > > I'm not sure what your question is. The vertex coordinates are in an RAS > > coordinate system, with the origin at the center of the volume (voxel > > 127.5,127.5,127.5 I think). The voxel coords are arranged in coronal > > slices, which I think you have figured out. > > > > cheers, > > Bruce > > > > -------------------------------------------------------- > > Bruce Fischl email: [EMAIL PROTECTED] > > Mass. General Hosp. NMR Center. tel:(617)-726-4897 > > Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 > > Charlestown, MA 02129 USA > > > > > > > > On Thu, 7 Mar 2002, Albert Kim wrote: > > > > > > > > > > > Hi Bruce, > > > > > > Very sorry but I'm still confused. When I click on a point in > > > TKSURFER and then SAVE the point, I see the following effect on the > > > logs (NOTE: this vertex happens to be the 0th Vertex): > > > > > > surfer: dmin=0.0569, 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) > > > > > > If I goto this point in Tkmedit, I land at the following "Volume > > > Index": 116, 136, 39 > > > which are voxel coords. Now, I see that these voxel coords can be > > > transformed into the "ORIGINAL" coords above by swapping the second > > > and third dimensions and offsetting things by 127.5. > > > -116 + 127.5 = 11.5 > > > 39 - 127.5 = -88.5 > > > -136 + 127.5 = -8.5 > > > > > > And I can see that these "ORIGINAL" coordinates are what are called > > > the "Volume RAS" coords in TKMEDIT and "Vertex RAS" in TKSURFER. But > > > I still do not understand the x,y,z coordinates: > > > surfer: dmin=0.0569, vno=0, x=-32.9801, y=-124.2833, z=-37.1158 > > > > > > These xyz coordinates are the output I see when I use mris_convert to > > > convert my rh.inflated surface into ascii format. For instance the > > > first row of the rh.inflated.ascii file is: > > > -32.980091 -124.283272 -37.115761, which is the same as the > > > stuff above. > > > > > > I apologize if I'm missing something obvious here. > > > Al > > > > > > > > > > > > > > > On Wed, 6 Mar 2002, Bruce Fischl wrote: > > > > > > > Hi Al, > > > > > > > > the matrix to convert row,col,slice voxel coords into the vertex > > > > coordinates (which are RAS in the COR file coordinate system with the > > > > origin at the center of the volume) should be: > > > > > > > > -1 0 0 128.5 > > > > 0 1 -128.5 > > > > 0 -1 0 128.5 > > > > > > > > > > > > we have been plagued by off-by-ones and off-by-1/2s, but I think this is > > > > correct. > > > > > > > > cheers, > > > > Bruce > > > > > > > > -------------------------------------------------------- > > > > Bruce Fischl email: [EMAIL PROTECTED] > > > > Mass. General Hosp. NMR Center. tel:(617)-726-4897 > > > > Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 > > > > Charlestown, MA 02129 USA > > > > > > > > > > > > > > > > On Wed, 6 Mar 2002, Albert Kim wrote: > > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
