Uploading the resulting NifTi files failed, twice. I guess this information will have
to suffice. My concern is, same program + same arguments = seriously different results.
I suppose the difference wouldn't matter, if it was consistent across scan types. The
anatomical data gets a coordinate set using the newer AFNI which is consistent with
EPI and anatomical data processed with the older to3d. The end result, using the
latest AFNI, is functional data sets which require a manual spatial tranlation to begin an
alignment to the anatomical data acquired in the same session.
Yes, I tries 3drefit -xorigin cen -yorigin cen -zorigin cen hoping that centering
the origins would bring the func/anat images closer. No dice. The bottom slice of the
functional(overlay) still shows up at the very top of the anatomical(underlay).

$ to3d -prefix T2.nii 002/*.dcm
$ to3d -time:zt 27 180 2000 alt-z -epan -prefix NewAfni.nii 005/*.dcm
$ to3d -time:zt 27 180 2000 alt-z -epan -prefix OldAfni.nii 005/*.dcm

$ 3dinfo -short T2.nii
++ 3dinfo: AFNI version=AFNI_2007_05_29_1644 (Aug 22 2007) [32-bit]
qform not present, sform used.
sform was not exact, and the worst axis is
4.175795 degrees from plumb.

Dataset File: T2.nii
Identifier Code: XYZ_9WfwteDUnKzIIVk3Q9ACFg Creation Date: Fri Sep 21 10:46:50 2007
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Superior-to-Inferior [-orient RAS]
R-to-L extent: -117.426 [R] -to- 101.715 [L] -step- 0.859 mm [256 voxels]
A-to-P extent: -129.092 [A] -to- 90.049 [P] -step- 0.859 mm [256 voxels]
I-to-S extent: -41.321 -to- 88.679 [S] -step- 5.000 mm [ 27 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: 0 to 3231


$ 3dinfo -short NewAfni.nii
++ 3dinfo: AFNI version=AFNI_2007_05_29_1644 (Aug 22 2007) [32-bit]
qform not present, sform used.
sform was not exact, and the worst axis is
4.175795 degrees from plumb.

Dataset File: NewAfni.nii
Identifier Code: XYZ_Rg_-s5QEsqqTx7xHTKVLBw Creation Date: Fri Sep 21 10:09:56 2007
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -115.592 [R] -to- 100.971 [L] -step- 3.437 mm [ 64 voxels]
A-to-P extent: -127.497 [A] -to- 89.065 [P] -step- 3.438 mm [ 64 voxels]
I-to-S extent: 88.624 [S] -to- 218.624 [S] -step- 5.000 mm [ 27 voxels]
Number of time steps = 180 Number of values at each pixel = 1
Time step = 2.000s Origin = 0.000s Number time-offset slices = 27 Thickness = 5.000
-- At sub-brick #0 '?' datum type is short: 0 to 1790

$ 3dinfo -short OldAfni.nii
++ 3dinfo: AFNI version=AFNI_2007_03_06_0841 (Mar 31 2007) [32-bit]

Dataset File: OldAfni.nii
Identifier Code: XYZ_rbKTeSnlDS5u4KxjIgoO9g Creation Date: Fri Sep 21 10:11:59 2007
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -154.324 [R] -to- 62.239 [L] -step- 3.438 mm [ 64 voxels]
A-to-P extent: -89.229 [A] -to- 127.334 [P] -step- 3.438 mm [ 64 voxels]
I-to-S extent: -44.812 -to- 85.188 [S] -step- 5.000 mm [ 27 voxels]
Number of time steps = 180 Number of values at each pixel = 1
Time step = 2.000s Origin = 0.000s Number time-offset slices = 27 Thickness = 5.000
-- At sub-brick #0 '?' datum type is short: 0 to 1790