Thanks Bob: I followed your suggestion and redid the to3d command, and the results of the T1 data looks great! The voxel resolution automatically becomes 0.902 x 0.902 x 1 mm, and I got the desired look of the T1 image.

But the same old coregistration problem did not go away! I opened two afni windows, and realized that not only did the left-right directions were reversed, the crosshairs are totally off between the anat and epi. I guess I can do either (a) nudge the anatomical (plus left-right reversal) to fit the epi (but guess it would fail because the two are really far OFF!); or (b) redo the to3d command on the epi. But do I have to? Here were the 3dinfo of the current epi:

++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Sep 30 2008) [32-bit]

Dataset File: yhh_r1_alt+z+orig
Identifier Code: AFN_8RxzgZMY0UyPvyqrmqHnLQ Creation Date: Sat Apr 4 07:34:41 20
09
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 38400000 (38 million) bytes
Geometry String: "MATRIX(3,0,0,-122.9264,0,3,0,-145.1,0,0,5,82.2):80,80,20"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -122.926 [R] -to- 114.074 [L] -step- 3.000 mm [ 80 voxels]
A-to-P extent: -145.100 [A] -to- 91.900 [P] -step- 3.000 mm [ 80 voxels]
I-to-S extent: 82.200 [S] -to- 177.200 [S] -step- 5.000 mm [ 20 voxels]
Number of time steps = 150 Time step = 2.000s Origin = 0.000s Number time-offse
t slices = 20 Thickness = 5.000
-- At sub-brick #0 '#0' datum type is short: 0 to 2750
-- At sub-brick #1 '#1' datum type is short: 0 to 2734
-- At sub-brick #2 '#2' datum type is short: 0 to 2757
** For info on all 150 sub-bricks, use '3dinfo -verb' **

compared to the newly saved anat2+orig

Dataset File: yhh_anat2+orig
Identifier Code: AFN_Yl1QBLn9DPMc3FEWAsFcKQ Creation Date: Sat Apr 4 06:53:53 2009
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 21233664 (21 million) bytes
Geometry String: "MATRIX(0.902778,0,0,-132.9264,0,0.902778,0,-146.7432,0,0,-1,98.19899):288,288,128"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Superior-to-Inferior [-orient RAS]
R-to-L extent: -132.926 [R] -to- 126.171 [L] -step- 0.903 mm [288 voxels]
A-to-P extent: -146.743 [A] -to- 112.354 [P] -step- 0.903 mm [288 voxels]
I-to-S extent: -28.801 -to- 98.199 [S] -step- 1.000 mm [128 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 3283

It seems to me that the I-to-S extent of the two datasets are different (especially problematic was the epi), but how can I fix this?

again, I put the screen snapshot of the afni windows showing these two files:
[myweb.ncku.edu.tw]

thx, chun-chia

p.s. oh Bob, forget to answer your previous Q: the slice thickness should be 128 mm (based on the fact that the epi has 20 slices of 5mm-think = 100mm).