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

[Dženan Zukić]

If I remember correctly, X index varies quickest. But yes, setting proper
values into the direction matrix should solve your problem.

Dženan

On Sat, Dec 18, 2010 at 01:16, David Nichols <dnichols at sourcesignal.com>wrote:

>  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>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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