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observed that if you compose transforms, you might observe artifacts<br>
such as torsional twisting of geometry.<br>
<br>
This torsional twist happens due to the geometry of the image object<br>
in 3D from which two consecutive slices of a 3D object are drawn. The<br>
slices hold slightly different geometries that cause a very small<br>
rotation. This rotation bias builds up as you compose.<br>
<br>
Kishore<br>
<br>
On Thu, Oct 15, 2009 at 5:20 PM, Darren Weber<br>
<div class=3D"im">&lt;<a href=3D"mailto:darren.weber.lists at gmail.com">darre=
n.weber.lists at gmail.com</a>&gt; wrote:<br>
&gt;<br>
</div><div><div></div><div class=3D"h5">&gt; We have a series of several th=
ousand 2D microscope images:<br>
&gt;<br>
&gt; img0001 ... imgN<br>
&gt;<br>
&gt; A simple ITK program uses itkImageSeriesReader to stack the sequential=
<br>
&gt; images into a 3D volume for output to a .vtk file.=C2=A0 Without any<b=
r>
&gt; coregistration of the image series, the result is a mess (as expected)=
.<br>
&gt;<br>
&gt; Another ITK program runs registration algorithm(s) on consecutive pair=
s of<br>
&gt; images in the 2D image series (each pair of images is registered<br>
&gt; independently of any other images in the series).=C2=A0 It outputs a t=
ransform<br>
&gt; file for each image registration, using file names something like:<br>
&gt;<br>
&gt; img0002to0001.xfm<br>
&gt; img0003to0002.xfm<br>
&gt; etc.<br>
&gt;<br>
&gt; What is an efficient way to combine and apply these transforms using a=
n ITK<br>
&gt; pipeline to &#39;concatenate&#39; the image series into a 3D stack?<br=
>
&gt;<br>
&gt; My conception of how this might work, in outline, is:<br>
&gt;<br>
&gt; a)=C2=A0 begin with img0001<br>
&gt; apply transform: none<br>
&gt;<br>
&gt; b) add img0002 to the stack<br>
&gt; apply transform: img0002to0001.xfm<br>
&gt;<br>
&gt; c) add img0003 to the stack<br>
&gt; apply transform: img0002to0001.xfm<br>
&gt; apply transform: img0003to0002.xfm<br>
&gt; (How to concatenate transforms without resampling image data?)<br>
&gt;<br>
&gt; d) add img0004 to the stack<br>
&gt; apply transform: img0002to0001.xfm<br>
&gt; apply transform: img0003to0002.xfm<br>
&gt; apply transform: img0004to0003.xfm<br>
&gt; (How to concatenate transforms without resampling image data?)<br>
&gt;<br>
&gt; etc.<br>
&gt;<br>
&gt;<br>
&gt; In this conception of the problem, the pair-wise registration transfor=
ms are<br>
&gt; &#39;concatenated&#39; to propagate the registration through the entir=
e series.<br>
&gt; What is the most efficient way to do that in ITK?<br>
&gt;<br>
&gt; Is it possible (or reasonable) to associate a transform object (or fil=
e)<br>
&gt; with each &#39;element&#39; of an itkImageSeriesReader?=C2=A0 If not, =
is there another<br>
&gt; convention for creating an ITK filter pipeline or registration pipelin=
e?<br>
&gt;<br>
&gt; TIA and take care,<br>
&gt; Darren<br>
&gt;<br>
&gt;<br>
</div></div><div><div></div><div class=3D"h5">&gt; ________________________=
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</div></div></blockquote></div><br>

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