-3.42822 0.21499 0.15398 101.74103

-0.24476 -3.27187 -1.19314 135.02863

0.06182 -1.03201 3.81480 -30.98481

0.00000 0.00000 0.00000 1.00000

while "mri_info --vox2ras-tkr" gives:

-3.43750 0.00000 0.00000 110.00000

0.00000 0.00000 4.00000 -70.00000

0.00000 -3.43750 0.00000 110.00000

0.00000 0.00000 0.00000 1.00000

I would understand if the tkr-vox2ras only did flips and 90º rotations to put the data as close to RAS format as possible without having to interpolate, but the orientations produced by those 2 transformations are very different, with the rows and the slices essentially switched. I would guess that it has something to do with this explanation from Slide 5, but I don't quite understand it:

"Field-of-View based – only depends on the identity of columns, rows, and slices, the number of voxels in each dimension, and their sizes. Unrelated to the “true” geometry but is an RAS coordinate system when the volume is “Coronally” sliced, which is the based “conformed” orientation in FreeSurfer."

Any additional clarity you could provide would be appreciated.

2) In Freesurfer XYZ space, why are the volumes centered at (# of voxels)/2? I would think that centering at ((# of voxels) + 1) /2 would put the true center of the volume on the origin.

Thanks again,

Clark

On Sep 20, 2011, at 2:14 PM, Douglas N Greve wrote:

Hi Clark, have you looked at this documentation yet?
http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt
doug
Clark Fisher wrote:
Hello,

I was wondering what orientation conventions are used when calculating the affine transformation matrix in register.dat. For an example, I'll use the data from subject 101 of the fsfast tutorial. According to mri_info, the functional volume is in LPS orientation, and the processed anatomical volume (T1.mgz) is in LIA orientation. Does the matrix in register.dat convert from the functional LPS orientation to the anatomical LIA orientation, or does the matrix assume these volumes are already transformed in some other way?

Thanks,
Clark
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