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Neil Killeen wrote:
> I have a DICOM image which I have converted to Analyze (with SPM2) and 
> NIFTI (with the LONI debabeler).

Hi Neil,

It might be better to go directly from DICOM to NIfTI, since this 
conversion can preserve some information that Analyze will lose (e.g. 
the NIfTI qform can hold the DICOM voxel-world mapping).

It sounds like the debabeler should be able to do this, alternatively 
try SPM5, dcm2nii, dinifti or one of the other tools listed here:

http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html

Having said that...

 > The labels in both cases are correct

...I think this is all that matters. I wouldn't worry too much about 
the exact choice of display axes in FSLVIEW, as long as the axis 
labels are right.

Best,
Ged.