[MINC-users] MINC 2.0 coordinate system

[Peter Neelin]

On Dec 20, 2012 1:34 AM, "Soren Christensen" <sorench at gmail.com> wrote:

>  In the MINC 2.0 coordinate system section of
>
http://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference#MINC_2.0_Structural_Attributes
> there is mention of "Startx, Starty and Startz" - just after the line
> "and the origin (0,0,0) in voxel coordinates is located at world
> coordinates (ox,oy,oz) as given by:"
>
> I got a bit confused here. The Start values for x y and z that we see
> using mincinfo are the world coordinates (referred to as "o") in that
> section right?

Nope. The start values are as described in that section (assuming that the
matrix order is fixed). Only when the direction cosines are the non-rotated
([1 0 0], [0 1 0], [0 0 1]) do the start values match the origin.

This convention was chosen so that applications that ignore direction
cosines will have the correct origin in the rotated frame (start and step
are expressed along the dimension and are self-consistent). Applications
that want to use the full coordinate information can do the right thing -
it is not hard, and you will almost certainly already have code doing
matrix math, so what is a little more?

> Isn't the order of these matrix multiplications the wrong way around by
the way?

Yup. That should be fixed.

Peter
--
Peter Neelin
peter.neelin at gmail.com