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

[Richard Beare]

I think that most of the transform types have a Compose method so you
can compute the transform between your first slice and any other.

On Fri, Oct 16, 2009 at 2:30 PM, Xiaofeng Z <xf10036 at hotmail.com> wrote:
> 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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