[Insight-users] Constructing 3D stack from 2D image series (withregistration)

[Xiaofeng Z]

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.


From: Darren Weber 
Sent: Thursday, October 15, 2009 5:20 PM
To: ITK Users 
Subject: [Insight-users] Constructing 3D stack from 2D image series (withregistration)



We have a series of several thousand 2D microscope images:

img0001 ... imgN

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).

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:

img0002to0001.xfm
img0003to0002.xfm
etc.

What is an efficient way to combine and apply these transforms using an ITK pipeline to 'concatenate' the image series into a 3D stack?

My conception of how this might work, in outline, is:

a)  begin with img0001
apply transform: none

b) add img0002 to the stack
apply transform: img0002to0001.xfm

c) add img0003 to the stack
apply transform: img0002to0001.xfm
apply transform: img0003to0002.xfm
(How to concatenate transforms without resampling image data?)

d) add img0004 to the stack
apply transform: img0002to0001.xfm
apply transform: img0003to0002.xfm
apply transform: img0004to0003.xfm
(How to concatenate transforms without resampling image data?)

etc.


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?

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?

TIA and take care,
Darren




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