[Insight-users] Registration of Slices

[Shekhar Chandra]

  Hi Everyone,

I'm a VTK user who is new to ITK. In my current project I have to 
register a stack or series of Micro CT images, which will be used to 
reconstruct some biological samples.

Via ITK I have worked out how to load the series (using the ImageSeries 
class, Multi-page TIFFs or MRC files). Traverse and filter (if 
necessary) the slices (using ImageSliceConstIteratorWithIndex and 
JoinSeriesImageFilter, as well as the itkSliceBySliceImageFilter). I put 
some of this on my blog for reference for those that are interested.
<http://l3mmings.blogspot.com/2010/08/slices-stacks-and-itk.html>

The problem I have is that registering the slices give me barely 
adequate results. I went about it by using the Multi-res example and 
Software Guide.

I make the first slice the fixed image and treat the next slice as the 
moving image. I transform/resample the moving image after registering it 
and make it the next fixed image. The next slice is then the moving 
image. I realise that the error in registration propagates using this 
method. Is this the best way to register slices?

On one post, it was suggested that one could use a sliding window (e.g. 
register slice before and after with fixed slice), but it was not 
mentioned how to do this. Has someone solved this problem or encountered it?

I know the parameters for registration are data dependent and have to be 
found. But when exploring a metric with a slice (as per Exploring a 
Metric example), it takes a while to compute even for -50 to 50 pixel 
translations for small images (300x300, few minutes for MeanSquares on a 
Core2duo with Optimised Registration methods). Is this normal?

Finally, what is the best way to do very coarse alignment in ITK? Center 
of Gravity sounds good, but it has rotations (because of the 
CenteredRigid2DTransform) and I do not need rotations.

Searching the web has not yielded any further help. Any suggestion or 
advice would be greatly appreciated.

Cheers
Shakes
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