[MINC-users] MINC convention for oblique imaging

[Andrew Janke]

> By MINC definition, xyz dimensions are defined in patient coordinates

Um maybe? :)  I always was of the opinion that the world co-ordinates
referred to the scanner. And thus 0,0,0 for a MRI machine is at the
centre of the gradients and 0,0,0 on some PET machines is at the
patients feet.

> and direction cosines are recommended to be the identity matrix.

If you add this into the mix then perhaps the top statement makes more sense.

> Therefore, in an oblique dataset, do MINC xyz dimensions refer to
> patient coordinates or MRI voxel coordinates? If the latter, is the MRI
> convention of readout='x', phase encoding='y', and slab encoding='z'
> also used by MINC?

No, and as far as I am aware there is no way you can guarantee that
phase will be y and slab in z. I think this sort of thinig is what
gets "other" file formats in trouble.  Yes most imaging sequences
might use this order but there is no way that you can guarantee this.
I certainly remember going through all sorts of contortions converting
bruker format data in which this sort of thing is/can be a convention.

> If the latter, then how to reconcile the
> inconsistency in coordinate definition between 'cor','sag' and 'trans'
> on the one hand and 'oblique' on the other?

The answer to this is to just think of the MINC world space as a
sampling of the scanner, if a patient head happens to be in there then
good and well. :)  Of course this does beg the question of why there
are -coronal type options in MINC but my answer to this would be "ease
of use for 90% of users"


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Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883