I have a dataset that i converted from .mgz to nii format using freesurfers mri_convert.

The structural dataset somes up wrong in afni. The axial window shows the coronal view, the
sagittal shows the axial images, and the coronal shows the sagittal images.

The info in the header says the data is SLA format.

I was thinking i could fix this by running 3drefit with the -orient ASL command.

first, i am not sure if this is the right order to put after the flag.

Regardless, when i run it, it seems to run, but nothing changes in the header, structural comes up
the same way in afni.

3drefit -orient ASL test+orig.nii
++ 3drefit: AFNI version=AFNI_2008_02_01_1144 (Feb 29 2008) [32-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as test+orig.nii,
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:test+orig.nii is 23.199993 degrees from plumb.
++ Processing AFNI dataset test+orig.nii
++ 3drefit processed 1 datasets



This structural is rotated. I put it into freesurfer, used their manual registration program
tkregister to rotate this to match my functionals (in order to get better alignment then just using
the header information to obliquify the structrual).


This is the output of 3dinfo:

++ 3dinfo: AFNI version=AFNI_2008_02_01_1144 (Feb 29 2008) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as test+orig.nii.gz,
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:test+orig.nii.gz is 23.199993 degrees from plumb.

Dataset File: test+orig.nii.gz
Identifier Code: NII_Jqhv8wcLLt28rSQlCYNSFA Creation Date: Thu Mar 6 09:33:31 2008
Dataset Type: Anat Bucket (-abuc)
Byte Order: MSB_FIRST {assumed} [this CPU native = MSB_FIRST]
Storage Mode: NIFTI file
Storage Space: 20971520 (21 million) bytes
Geometry String: "MATRIX(0.393942,-0.919136,0,1.259338,0,0,1,-83.16264,-0.919135,-
0.393942,0,162.0646):256,256,160"
Data Axes Tilt: Oblique (23.200 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Superior-to-Inferior
second (y) = Left-to-Right
third (z) = Anterior-to-Posterior [-orient SLA]
R-to-L extent: -253.741 [R] -to- 1.259 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -83.163 [A] -to- 75.837 [P] -step- 1.000 mm [160 voxels]
I-to-S extent: -92.935 -to- 162.065 [S] -step- 1.000 mm [256 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: 0 to 1355

----- HISTORY -----


Any suggestions appreciated.

Thanks,
Stephanie McMains