[MINC-users] Wikibook coordinate conversion documentation fixed

[Alex Zijdenbos]

Hi Tarek,

Nice work! It's good to have this coordinate business straightened out once
and for all, as it is invariably problematic, especially for new MINC users
- and in fact, I am not sure I'd ever wrapped my head completely around the
direction cosines bit :-)

I do however have a few suggestions:

1) to add a diagram that illustrates the coordinate systems. I'm pretty
sure that exists somewhere, but right now I don't remember exactly where I
saw that. If somebody knows where it is I would suggest to add it to this
section.

2) what is not clear/missing is how one goes from real (as in, floating
point) voxel coordinates to integer array indices. I believe that is a
rounding operation (as opposed to a truncation for example).

3) Related to 2), we may want to clarify explicitly here that a MINC image
is a lattice of point samples, which I think is often not obvious to
people. In this context, the statement: "The voxel coordinate values are
nonnegative integers ranging from zero to one less than the number of data
points along the axis, with the origin fixed at one corner of the image"
may be confusing to some: if you consider the step size as the "width" of a
voxel (which I think most people would do), then the voxel coordinate
origin is actually half a voxel into the image, or conversely, what people
might consider the "corner" of a standard MNI 1.00mm image, actually has
voxel coordinates (-0.5, -0.5, -0.5), which is also _not_ the start
coordinate.

-- A


On Sat, Jun 14, 2014 at 5:47 AM, Tarek Sherif <tarek.sherif at mcgill.ca>
wrote:

> Hello all,
>
> After some discussion with Bert Vincent, it became clear
> that the conversion equations in the Wikibook
> documentation were completely wrong. I've fixed them
> and added some other information that I thought might
> be useful to people: https://en.wikibooks.org/wiki/
> MINC/Reference/MINC2.0_File_Format_Reference#MINC_2.0_coordinate_system
>
> The information added includes:
> 1. The decomposition of the voxel-to-world transformation
> into scaling, rotation and translation components.
> 2. The inverse, world-to-voxel transformation.
>
> If people could verify the correctness of the new
> equations, that would be great.
>
> Tarek
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>