Dear Afni Gurus,

I created the volumes anatomical and epi data using to3d. I am running to two issues here,

1. When i ran 3dinfo on the BRIK's, it shows that both the data are oblique.

3dinfo of anat:

Identifier Code: XYZ__mSJvXb3U22V6QVDTe0tpg Creation Date: Wed Aug 15 13:56:09 2012
Template Space: ORIG
Dataset Type: MRI Anatomy (-anat)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 29,286,400 (29 million) bytes
Geometry String: "MATRIX(0.8,0.01117,-1.04026e-10,-90.2304,-0.011098,0.79478,0.090571,-173.0387,0.001264,-0.090554,0.794935,-49.88791):220,320,208"
Data Axes Tilt: Oblique (6.549 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: -90.230 [R] -to- 84.970 [L] -step- 0.800 mm [220 voxels]
A-to-P extent: -173.039 [A] -to- 82.161 [P] -step- 0.800 mm [320 voxels]
I-to-S extent: -49.888 I -to- 115.712 S -step- 0.800 mm [208 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 2659

3dinfo of epi:

Storage Space: 538,312,704 (538 million) bytes
Geometry String: "MATRIX(1.71875,0,0,-110,0,1.695178,0.66019,-138.0019,0,-0.283676,3.945143,-35.90817):128,128,37"
Data Axes Tilt: Oblique (9.500 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: -110.000 [R] -to- 108.281 [L] -step- 1.719 mm [128 voxels]
A-to-P extent: -128.950 [A] -to- 89.331 [P] -step- 1.719 mm [128 voxels]
I-to-S extent: -54.063 I -to- 89.937 S -step- 4.000 mm [ 37 voxels]
Number of time steps = 444 Time step = 2.00000s Origin = 0.00000s Number time-offset slices = 37 Thickness = 4.000
-- At sub-brick #0 '#0' datum type is short: 0 to 2366
-- At sub-brick #1 '#1' datum type is short: 0 to 2483
-- At sub-brick #2 '#2' datum type is short: 0 to 2466
** For info on all 444 sub-bricks, use '3dinfo -verb' **

2. The data does not align properly.

So, my question is:

1. Can I run 3dWarp -deoblique on the anatomy and epi separately? Will it take care of making the data axes to cardinal space?

2. Since there is alignment issue, I am planning to run the align_epi_anat.py script to fix the problem. If I choose to keep '-deoblique on', will it fix the obliquity in anatomy and epi?

Thank you,
Hema



Edited 2 time(s). Last edit at 08/20/2012 09:23PM by rick reynolds.