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<DIV><FONT face=Calibri>There must be a way to combine the transformations
together before applying the combined transformation to the image.
Otherwise, after hundreds of interpolation, imageN will probably not have much
information left.</FONT></DIV>
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<DIV><FONT face=Calibri size=3></FONT><FONT face=Calibri
size=3></FONT><BR></DIV>
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<DIV style="font-color: black"><B>From:</B> <A
title=darren.weber.lists@gmail.com
href="mailto:darren.weber.lists@gmail.com">Darren Weber</A> </DIV>
<DIV><B>Sent:</B> Thursday, October 15, 2009 5:20 PM</DIV>
<DIV><B>To:</B> <A title=insight-users@itk.org
href="mailto:insight-users@itk.org">ITK Users</A> </DIV>
<DIV><B>Subject:</B> [Insight-users] Constructing 3D stack from 2D image series
(withregistration)</DIV></DIV></DIV>
<DIV><BR></DIV><BR>We have a series of several thousand 2D microscope
images:<BR><BR>img0001 ... imgN<BR><BR>A simple ITK program uses
itkImageSeriesReader to stack the sequential images into a 3D volume for output
to a .vtk file. Without any coregistration of the image series, the result
is a mess (as expected).<BR><BR>Another ITK program runs registration
algorithm(s) on consecutive pairs of images in the 2D image series (each pair of
images is registered independently of any other images in the series). It
outputs a transform file for each image registration, using file names something
like:<BR><BR>img0002to0001.xfm<BR>img0003to0002.xfm<BR>etc.<BR><BR>What is an
efficient way to combine and apply these transforms using an ITK pipeline to
'concatenate' the image series into a 3D stack?<BR><BR>My conception of how this
might work, in outline, is:<BR><BR>a) begin with img0001<BR>apply
transform: none<BR><BR>b) add img0002 to the stack<BR>apply transform:
img0002to0001.xfm<BR><BR>c) add img0003 to the stack<BR>apply transform:
img0002to0001.xfm<BR>apply transform: img0003to0002.xfm<BR>(How to concatenate
transforms without resampling image data?)<BR><BR>d) add img0004 to the
stack<BR>apply transform: img0002to0001.xfm<BR>apply transform:
img0003to0002.xfm<BR>apply transform: img0004to0003.xfm<BR>(How to concatenate
transforms without resampling image data?)<BR><BR>etc.<BR><BR><BR>In this
conception of the problem, the pair-wise registration transforms are
'concatenated' to propagate the registration through the entire series.
What is the most efficient way to do that in ITK?<BR><BR>Is it possible (or
reasonable) to associate a transform object (or file) with each 'element' of an
itkImageSeriesReader? If not, is there another convention for creating an
ITK filter pipeline or registration pipeline?<BR><BR>TIA and take
care,<BR>Darren<BR><BR>
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