I'm having a similar problem with a variety of templates sent by a collaborator in NIFTI format. Basically it seems like the Y axis is flipped -- the back of the brain is on the left in the sagittal view, where it's usually on the right. Attached is the 3dinfo readout from one of the templates. I've tried the nifti_tool + 3dresample approach without success; neither -orient lpi (supposedly the AFNI default) nor -orient rai (what the TT_N27 brain actually displays in 3dinfo) actually changes the displayed orientation of the image. Any ideas?


Thanks,
Matt

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babel-17:ANTSanalysis mweb$ 3dinfo BOLDtemplategm.nii.gz
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (May 25 2012) [64-bit]

Dataset File: BOLDtemplategm.nii.gz
Identifier Code: NII_pE0C3g2ASEJhz2LuhwTb6w Creation Date: Tue May 29 17:34:35 2012
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 655,360 (655 thousand) bytes
Geometry String: "MATRIX(3,0,0,-102.0013,0,3,0,43.55731,0,0,3,-35.65765):64,64,40"
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: -102.001 [R] -to- 86.999 [L] -step- 3.000 mm [ 64 voxels]
A-to-P extent: 43.557 [P] -to- 232.557 [P] -step- 3.000 mm [ 64 voxels]
I-to-S extent: -35.658 -to- 81.342 [S] -step- 3.000 mm [ 40 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float