Hi Colm,

I don't think there are any problems here.

Identical datasets should look identical in AFNI, regardless of
which of the 48 orientations they happen to have. AFNI makes a
sagittal image look sagittal. While 3dresample may change the
order of the data on disk, it should look the same in AFNI.

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FSL should not require LPI data when dealing with NIfTI datasets
(it would when using ANALYZE datasets). So the 3dresample command,
while not harmful, may not do anything useful, either.

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I know little of how FSL evaluates a dataset as being NEUROLOGICAL,
though I can guess (right-handed, maybe). It may even have some
user interface variable to flip the image in the viewer.

In any case, I suggest you rely on what is left in AFNI, and then
visually verify that it is on the same side in FSL.

- rick