Hello AFNI users,

I ran into a problem when de-oblique-ing both my anat and func data set(see fig below,column 1,2d/SE;column 2,3d; column 3, epi;column 4, epi upon 3d,both before deobliqueing; colum 5, after deobliquing, epi upon 3d): It is easy to see, before deobliqueing, the func data overlay well upon 3d, but after deobliqueing, the func stayed beyond the 3d.


I tried the methods as posted in
[afni.nimh.nih.gov]

but it didn't work.
I downloaded the 2008-07-18-1710 version of liunux_gcc32 beforehand and replaced the older files instead of deleting them; my 1.13 version align_epi_anat_py stuck at skullstrip so I gave up triyng align_anat_epi. I am novice so please make your suggestions as operational as possible. Thanks in advance!

THE FOLLOWING ARE info FROM 3dinfo:

2d/SE:
[root@localhost s2]# 3dinfo s2-2d+orig
++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Oct 23 2008) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./s2-2d+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./s2-2d+orig.BRIK is 3.061006 degrees from plumb.

Dataset File: s2-2d+orig
Identifier Code: XYZ_J9IoznakuYm2IYtFpL-wyA Creation Date: Mon Oct 27 00:08:142008
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 9175040 (9.2 million) bytes
Geometry String: "MATRIX(0.42928,0.011991,-0.183676,-96.77007,-0.012585,0.42913,-0.229174,-118.3354,-0.013831,-0.018308,-5.492153,97.18745):448,512,20"
Data Axes Tilt: Oblique (3.061 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Superior-to-Inferior [-orient RAS]
R-to-L extent: -96.770 [R] -to- 95.300 [L] -step- 0.430 mm [448 voxels]
A-to-P extent: -118.335 [A] -to- 101.235 [P] -step- 0.430 mm [512 voxels]
I-to-S extent: -7.313 -to- 97.187 [S] -step- 5.500 mm [ 20 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 3194

----- HISTORY -----
[root@localhost.localdomain: Mon Oct 27 00:07:37 2008] to3d 100002100310001 100002100310002 100002100310003 ... 100002100310019 100002100310020

3d:
[root@localhost s2]# 3dinfo s2-3d+orig
++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Oct 23 2008) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./s2-3d+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./s2-3d+orig.BRIK is 5.280418 degrees from plumb.

Dataset File: s2-3d+orig
Identifier Code: XYZ_DJ3Wt_GcSEfzpLI33OoxIw Creation Date: Mon Oct 27 00:09:032008
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 12582912 (13 million) bytes
Geometry String: "MATRIX(0.074899,-0.025397,1.692786,-85.54032,0.856105,0.002222,-0.1481,-112.5055,0,-0.858997,-0.050433,126.2026):256,256,96"
Data Axes Tilt: Oblique (5.280 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Anterior-to-Posterior
second (y) = Superior-to-Inferior
third (z) = Right-to-Left [-orient ASR]
R-to-L extent: -85.540 [R] -to- 75.960 [L] -step- 1.700 mm [ 96 voxels]
A-to-P extent: -112.506 [A] -to- 106.635 [P] -step- 0.859 mm [256 voxels]
I-to-S extent: -92.938 -to- 126.203 [S] -step- 0.859 mm [256 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 1080

----- HISTORY -----
[root@localhost.localdomain: Mon Oct 27 00:08:25 2008] to3d 100002100210001 100002100210002 100002100210003 ... 100002100210095 100002100210096

epi:
[root@localhost s2]# 3dinfo s2-runall+orig
++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Oct 23 2008) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./s2-runall+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./s2-runall+orig.BRIK is 3.061006 degrees from plumb.

Dataset File: s2-runall+orig
Identifier Code: XYZ_lIUjDHC3oVr7q3LW995ixg Creation Date: Mon Oct 27 00:12:152008
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 73728000 (74 million) bytes
Geometry String: "MATRIX(3.434243,0.095927,0.183676,-108.742,-0.100681,3.433038,0.229174,-116.2665,-0.110651,-0.14646,5.492153,97.50151):64,64,20"
Data Axes Tilt: Oblique (3.061 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -122.369 [R] -to- 94.194 [L] -step- 3.438 mm [ 64 voxels]
A-to-P extent: -104.474 [A] -to- 112.088 [P] -step- 3.438 mm [ 64 voxels]
I-to-S extent: -14.948 -to- 89.552 [S] -step- 5.500 mm [ 20 voxels]
Number of time steps = 450 Time step = 2.000s Origin = 0.000s Number time-offset slices = 20 Thickness = 5.500
-- At sub-brick #0 '#0' datum type is short: 0 to 1870
-- At sub-brick #1 '#1' datum type is short: 0 to 1810
-- At sub-brick #2 '#2' datum type is short: 0 to 1801
** For info on all 450 sub-bricks, use '3dinfo -verb' **

----- HISTORY -----
[root@localhost.localdomain: Mon Oct 27 00:11:00 2008] to3d -time:zt 20 450 2s altplus 100002100410001 100002100410002 100002100410003 ... 100002100410449 100002100410450