[Insight-users] Matching physical axes correctly on image read

[David Nichols]

Thanks for the clarification.  So, it's always true that X is axis 0 
(where the index varies most slowly), Y is axis 1 and Z is axis 2 (where 
the index varies most quickly).  So, all I need to do if apply an affine 
transform to change the axes to point into the desired direction.  For 
instance, something like
[[ 0,  0, 1, 0 ]
  [ -1, 0, 0, 0 ]
  [ 0,  1, 0, 0 ]
  [ 0,  0, 0, 1 ] ]
will do what I want.

David
> You need to use directions (transform matrix) in order to achieve all 
> that.
>
> X is the axis 0, Y 1 and Z 2, in image space. In world space they get 
> transformed using the said transform matrix (or directions + spacing).
>
> I am sure you can find much more info if you search for it.
>
> Regards,
> Dženan
>
> On Wed, Dec 15, 2010 at 19:20, David Nichols 
> <dnichols at sourcesignal.com <mailto:dnichols at sourcesignal.com>> wrote:
>
>     My 'natural', image index oriented coordinate system is left
>     handed.  I'm thinking that manipulating the itk origin and spacing
>     can put things in the correct order.
>
>     First, it seems that itk uses the C language index order, with the
>     rightmost index changing most quickly. So, if I had an image with
>     120 slices, each of which had 128 rows and 110 columns, I would
>     declare it in C as
>     short int Image[120][128][110];
>     I want to set the origin of the physical coordinate system at
>     voxel [0,0,0], with the x axis pointing in the direction of
>     decreasing row, the y axis pointing in the direction of increasing
>     column and the z axis pointing in the direction of increasing
>     slice.  If I look at Image[k][i][j], then increasing x decreases
>     i, increasing y increases j and increasing z increases k.
>
>     Two issues. First, the examples in The Guide seem to assume that x
>     goes with index 0, y with index 1 and z with index 2.  How do I
>     permute things to get them as described above?  Secondly, to make
>     an advancing row index point in the negative x direction, does one
>     make the spacing negative in that dimension?  (This seems logical
>     in one way and perverse in another.)  Finally, what would be the
>     correct entries to use in a metaheader file?  One can use
>
>     NDims = 3
>     DimSize = 110 128 120
>     ElementSize = 1 1 1
>
>     but this doesn't give the x/y/z axes oriented as desired.
>
>     I appreciate any advice you can provide.
>
>     David
>
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