below is the output of 3dinfo on the result of the 3dKruskalWallis and one of the nifti files from fsl. (the results of nifti_tool -disp_hdr -infiles vol0000.nii.gz are at the end in case it helps.)

What I've just noticed about the that afni thinks the vol0000 data set is LPI, however, all data that we feed into FSL is RPI and would not have been changed. Is this odd?

++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Jul 23 2008) [64-bit]

Dataset File: greyVbmKw+orig
Identifier Code: XYZ_YYMhdZIMx3WQS4mVRBkMhQ Creation Date: Mon Nov 24 14:55:47 2008
Dataset Type: Inten+ChiSq (-fict)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 3610516 (3.6 million) bytes
Geometry String: "MATRIX(-2,0,0,0,0,-2,0,0,0,0,2,0):91,109,91"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -180.000 [R] -to- 0.000 -step- 2.000 mm [ 91 voxels]
A-to-P extent: -216.000 [A] -to- 0.000 -step- 2.000 mm [109 voxels]
I-to-S extent: 0.000 -to- 180.000 [S] -step- 2.000 mm [ 91 voxels]
Number of values stored at each pixel = 2
-- At sub-brick #0 '#0' datum type is short: 0 to 32767 [internal]
[* 9.15555e-05] 0 to 3 [scaled]
-- At sub-brick #1 '#1' datum type is short: 0 to 1782 [internal]
[* 0.01] 0 to 17.82 [scaled]
statcode = fict; statpar = 2
Auxiliary functional statistical parameters:
DEGREES-of-FREEDOM
2

----- HISTORY -----
[colmconn@login02: Mon Nov 24 14:55:47 2008] 3dKruskalWallis -levels 3 -dset 1 vol0000.nii.gz -dset 1 vol0001.nii.gz -dset 1 vol0002.nii.gz -dset 1 vol0003.nii.gz -dset 1 vol0004.nii.gz -dset 1 vol0005.nii.gz -dset 1 vol0006.nii.gz -dset 1 vol0007.nii.gz -dset 1 vol0008.nii.gz -dset 2 vol0009.nii.gz -dset 2 vol0010.nii.gz -dset 2 vol0011.nii.gz -dset 2 vol0012.nii.gz -dset 2 vol0013.nii.gz -dset 2 vol0014.nii.gz -dset 2 vol0015.nii.gz -dset 2 vol0016.nii.gz -dset 2 vol0017.nii.gz -dset 3 vol0018.nii.gz -dset 3 vol0019.nii.gz -dset 3 vol0020.nii.gz -dset 3 vol0021.nii.gz -dset 3 vol0022.nii.gz -dset 3 vol0023.nii.gz -dset 3 vol0024.nii.gz -dset 3 vol0025.nii.gz -dset 3 vol0026.nii.gz -out greyVbmKw

*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file 'vol0000.nii.gz'

Dataset File: vol0000.nii.gz
Identifier Code: NII__bbCm77hzyAtkWoQ7iMnCQ Creation Date: Mon Nov 24 15:14:18 2008
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Storage Space: 3610516 (3.6 million) bytes
Geometry String: "MATRIX(2,0,0,0,0,2,0,0,0,0,2,0):91,109,91"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -180.000 [R] -to- 0.000 -step- 2.000 mm [ 91 voxels]
A-to-P extent: -216.000 [A] -to- 0.000 -step- 2.000 mm [109 voxels]
I-to-S extent: 0.000 -to- 180.000 [S] -step- 2.000 mm [ 91 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float


header file 'vol0000.nii.gz', num_fields = 43

all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr 0 1 348
data_type 4 10
db_name 14 18
extents 32 1 0
session_error 36 1 0
regular 38 1 r
dim_info 39 1 0
dim 40 8 3 91 109 91 1 1 1 1
intent_p1 56 1 0.0
intent_p2 60 1 0.0
intent_p3 64 1 0.0
intent_code 68 1 0
datatype 70 1 16
bitpix 72 1 32
slice_start 74 1 0
pixdim 76 8 0.0 2.0 2.0 2.0 1.0 0.0 0.0 0.0
vox_offset 108 1 352.0
scl_slope 112 1 1.0
scl_inter 116 1 0.0
slice_end 120 1 0
slice_code 122 1 0
xyzt_units 123 1 10
cal_max 124 1 3349.236084
cal_min 128 1 -148.571213
slice_duration 132 1 0.0
toffset 136 1 0.0
glmax 140 1 0
glmin 144 1 0
descrip 148 80 FSL4.0
aux_file 228 24
qform_code 252 1 0
sform_code 254 1 0
quatern_b 256 1 0.0
quatern_c 260 1 0.0
quatern_d 264 1 0.0
qoffset_x 268 1 0.0
qoffset_y 272 1 0.0
qoffset_z 276 1 0.0
srow_x 280 4 0.0 0.0 0.0 0.0
srow_y 296 4 0.0 0.0 0.0 0.0
srow_z 312 4 0.0 0.0 0.0 0.0
intent_name 328 16
magic 344 4 n+1