Hello,

I am getting strange behavior when running 3dcopy on some of my data files. The data is originally in LSB_FIRST. 3dcopy changes it to MSB_FIRST, and the image appears byte-swapped in the AFNI viewer. When I use 3dcalc (3dcalc -a Anat_1+orig -expr 'a' -prefix Anat_1_calc), then the byte order is MSB_FIRST but the data appears okay in the viewer.

3dcopy is used by align_epi_anat.py, and the byte-swapping issue caused the skull stripping to fail.

-Rasmus

3dinfo of original T1:

++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Jan 23 2015) [64-bit]

Dataset File: Anat_1+orig
Identifier Code: XYZ_CZg3Fg59fJ0kstnM5ECeXA Creation Date: Thu May 2 10:02:45 2013
Template Space: ORIG
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 20,447,232 (20 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-125.156,0,1,0,-158.906,0,0,1,-72.344):256,256,156"
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: -125.156 [R] -to- 129.844 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -158.906 [A] -to- 96.094 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -72.344 -to- 82.656 [S] -step- 1.000 mm [156 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 10449


-----------

3dinfo after running 3dcopy:

++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Jan 23 2015) [64-bit]

Dataset File: Anat_1_copy+orig
Identifier Code: XYZ_8j0N7KM9RlnxwWeZ5oVs7A Creation Date: Mon Jan 26 12:45:04 2015
Template Space: ORIG
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: MSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 20,447,232 (20 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-125.156,0,1,0,-158.906,0,0,1,-72.344):256,256,156"
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: -125.156 [R] -to- 129.844 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -158.906 [A] -to- 96.094 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -72.344 -to- 82.656 [S] -step- 1.000 mm [156 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 10449

-------
3dinfo after running 3dcalc:

++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Jan 23 2015) [64-bit]

Dataset File: Anat_1_calc+orig
Identifier Code: XYZ_VCub9Xic4Cu4aBhrLMosSg Creation Date: Mon Jan 26 12:47:08 2015
Template Space: ORIG
Dataset Type: Spoiled GRASS (-spgr)
Byte Order: MSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 20,447,232 (20 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,-125.156,0,1,0,-158.906,0,0,1,-72.344):256,256,156"
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: -125.156 [R] -to- 129.844 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -158.906 [A] -to- 96.094 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -72.344 -to- 82.656 [S] -step- 1.000 mm [156 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is short: 0 to 10449