> I have a set of Analyze images in radiologic (R=L) format.
>
> I want to spatially normalize these to a template in neurological (R=R)
> format.
>
> Spm_sn3d.m states, "The normalized images should use neurological
> orientation for their orientation"
>
> So, I carefully choose my normalization defaults so that the initial
> estimates for the affine transformation is radiologic [0 0 0 0 0 0 -1 -1 -1
> 0 0 0]
>
> However, when I run the normalization, the resulting display states,
> "Linear affine component - no flipping" - and the images appear left=right
> (which I presume to be incorrect, since SPM told me at this state
> everything should be in neurologic format)
>
> Can someone please shed some light on this? I've sifted through the
> archives, and while there is a lot of information about the orientation
> issue, nothing seems to address this specifically.
I don't fully understand what you did here. You flipped in three directions,
which should have resulted in a flipping of the co-ordinate system from a
left-handed to a right-handed system (flipping twice would be just a rotation).
In SPM99, flipping from a "radiologically" stored axial Analyze image, to a
"neurologically" oriented image, involves setting the initial estimates to
[0 0 0 0 0 0 -1 1 1 0 0 0]. This is a single flip in the x direction.
I don't really like the "neurological" and "radiological" notations. Left- and
right-handed makes a lot more sense for MRI data, which can be acquired in
any orientation.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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