Hi everybody,

I've got a question about converting NIfTI files for use with FSL.

I initially used to3d to convert Siemens IMA files to NIfTI using the following command line

to3d -anat -prefix 66101_2.anat.nii -session ../../../ts/ctrl/66101_2 mprage/0119-0009-0863.ima mprage/0119-0009-0864.ima mprage/0119-0009-0865.ima ... mprage/0119-0009-1051.ima mprage/0119-0009-1052.ima

3dinfo reports the following
++ 3dinfo: AFNI version=AFNI_2007_03_06_0841 (May 15 2007) [64-bit]

Dataset File: 66101_2.anat.nii
Identifier Code: XYZ_nv-mNQcs140vMbUNPHRong Creation Date: Wed Feb 7 16:25:18 2007
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI file
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Superior-to-Inferior
third (z) = Right-to-Left [-orient ASR]
R-to-L extent: -99.000 [R] -to- 90.000 [L] -step- 1.000 mm [190 voxels]
A-to-P extent: -127.500 [A] -to- 127.500 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -127.500 -to- 127.500 [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 4095

Now I want to use FSL to perform volumetric analyses using the new FSLVBM tools. As I understand it FSL likes files to be in LPI orientation. So I used 3dresample -orient LPI -prefix LPI.nii -inset 66101_2.anat.nii to do this job and 3dinfo now reports that the files LPI and they appear in the correct orientation in fslview.

However, while I was at it I performed the following conversion as well: 3dresample -orient RPI -prefix RPI.nii -inset 66101_2.anat.nii
when I load these files into the AFNI viewer they look identical. You can see this in the screen shot (LPI on top RPI on bottom) [tcin.tchpc.tcd.ie]

Another problem with these files is the following:
> fslorient -getorient LPI.nii
NEUROLOGICAL
> fslorient -getorient RPI.nii
RADIOLOGICAL

The files are at [tcin.tchpc.tcd.ie] [tcin.tchpc.tcd.ie] and the original data is at
[tcin.tchpc.tcd.ie]

This has me very confused: I do not know which side of the image is the left side of the brain. Can any one help?

Thanks,

Colm.