There are several "RAS" coordinates in tkmedit. One is scanner coords (vol2ras), the other is "volume RAS" coordinates (tkrvox2ras). doug

On 12/18/12 11:31 PM, octavian lie wrote:

Dear Douglas, yes, it matches the T1. I am interested though in matching the volume RAS as it appears in tkmedit, so I changed the code to use tkrvox2ras instead of vox2ras0. Thank you, octavian.

On Tue, Dec 18, 2012 at 10:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

That code looks correct. It should match the scanner coordinates.
Does the volume geometry (ie, vox2ras) in the labelMRI.mgz file
match that of the orig.mgz/T1.mgz?

doug


On 12/18/12 6:10 PM, octavian lie wrote:

...

        Dear Douglas,

I adapted the following script to get the RAS coordinates:
segmri = MRIread(labelMRI.mgz); %labelMRI is the input resection
volume .mgz
segid =1;
% Get list of voxels with seg id
indlab = find(segmri.vol == segid);
nlab = length(indlab);

% Convert indices to row, col, slice
[r c s] = ind2sub(segmri.volsize,indlab);
crs = [c r s]' - 1 ; % 0-based
crs = [crs; ones(1,nlab)];

% Convert row, col, slice to XYZ
xyz1 = segmri.vox2ras0 * crs;
xyz = xyz1(1:3,:)';
inspecting the xyz matrix, copying individual RAS coordinates
from xyz to tkmedit volume RAS field, and noting the RAS
coordinates of the boundaries in the R,A,S, directions, it looks
like x and y/ R and A are ok, but the S/z is off, closer in nos
with the volume scanner coordinates. I could not figure out why
this is. I mention that the labelMRI.mgz  was generated by using
mri_convert on a labelMRI.nii mask file imported from itksnap
without additional flags.
Please advise, I also mention that the labelMRI.mgz file aligns
well in tkmedit with the patient's T1.mgz.
Below I paste the mri_info on labelMRI.mgz
        type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r =
-0.2196
: x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 1.9029
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 28.2156

talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal

voxel to ras transform:
-1.0000 -0.0000 -0.0000 127.7804
-0.0000 0.0000 1.0000 -126.0971
0.0000 -1.0000 0.0000 156.2156
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform:
-1.0000 0.0000 0.0000 127.7804
-0.0000 -0.0000 -1.0000 156.2156
-0.0000 1.0000 -0.0000 126.0971
0.0000 0.0000 0.0000 1.0000
Thank you very much,
Octavian.

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