Rick,

In it's most basic sense, yes the alignment is not good. Attached is an image (hopefully) of the before and after auto-tlrc of our Anat file. You can see how midline of the brain is no longer plumb afterward the autotlrc. I wonder actually if the program somehow is not registering the 3drefit and going back to the orginal oblique angle. Though your idea about original distance being too far apart seems legit as well.



Here as well is the original img/hdr file's 3dinfo:
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Identifier Code: NII_ufbqXcZnnGpTQzUx0qO61Q Creation Date: Tue Jul 17 18:35:32 2012
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Storage Space: 5,242,880 (5.2 million) bytes
Geometry String: "MATRIX(0.999794,-0.008053,-0.074472,-130.6089,-0.003928,-0.977315,0.847019,87.28014,0.019901,0.211638,3.908582,-71.59802):256,256,40"
Data Axes Tilt: Oblique (12.273 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -130.609 [R] -to- 124.391 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -167.720 [A] -to- 87.280 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -71.598 -to- 84.402 [S] -step- 4.000 mm [ 40 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short
__________________________________________________________________________


Look forward to your thoughts.

Thanks again for your time

-chris