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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 <br>
[[ 0, 0, 1, 0 ]<br>
[ -1, 0, 0, 0 ]<br>
[ 0, 1, 0, 0 ]<br>
[ 0, 0, 0, 1 ] ]<br>
will do what I want.<br>
<br>
David<br>
<blockquote
cite="mid:AANLkTinVOYarH-u8r0jzZE3gaepv_9F9LzDGBW_LOm9Z@mail.gmail.com"
type="cite">You need to use directions (transform matrix) in order
to achieve all that.
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>I am sure you can find much more info if you search for it.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Dženan<br>
<br>
<div class="gmail_quote">On Wed, Dec 15, 2010 at 19:20, David
Nichols <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:dnichols@sourcesignal.com">dnichols@sourcesignal.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">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.<br>
<br>
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<br>
short int Image[120][128][110];<br>
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.<br>
<br>
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<br>
<br>
NDims = 3<br>
DimSize = 110 128 120<br>
ElementSize = 1 1 1<br>
<br>
but this doesn't give the x/y/z axes oriented as desired.<br>
<br>
I appreciate any advice you can provide.<br>
<br>
David<br>
<br>
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