[Elastix] Mimicking Fiji's Register_Virtual_Stack

S. Klein s.klein at erasmusmc.nl
Thu Aug 4 11:44:20 CEST 2016


Hi Roman,

Some suggestions:

1) The old post you refer to is still up-to-date. It seems a sensible 
recipe.

2) SIFT features are indeed not implemented in Elastix. If you have a 
method to do a rough but robust SIFT-based registration, which can 
export the resulting transformation, you could feed this transformation 
as initial transformation to Elastix, to help the registration a bit in 
case the misalignments are very large.

3) Elastix will not extend the canvas. It will use the fixed image's 
canvas as the target canvas. (not sure if I answered your question)

4) To simplify the scripting, you could consider to use SimpleElastix. 
http://simpleelastix.readthedocs.io/

Cheers, Stefan


On 25-07-2016 16:08, Grothausmann, Roman Dr. wrote:
> Dear mailing list members,
>
>
> Due to excessive memory needs of Fiji's Register_Virtual_Stack (as it 
> extents the resulting images to fully contain the original) I'm trying 
> to mimic Fiji's Register_Virtual_Stack (RVS) with elastix.
> From the web docs it seems that ITK/elastix has no direct 
> correspondence to the "Scale Invariant Feature Transform" (SIFT).
> What would be the closest alternative?
> Except for one old post 
> (https://cmake.org/pipermail/insight-users/2011-July/041773.html) I 
> could not find any instructions for elastix to do iterative 
> registration of images forming a stack.
> Does some kind of front-end exist to use elastix for stacks?
> How to mimic RVS best without extending the canvas but specifying a 
> ROI or cropping region?
>
> Many thanks for any help or hints
> Roman
> _______________________________________________
> Elastix mailing list
> Elastix at bigr.nl
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-- 
Stefan Klein
+31 10 7043442
http://www.bigr.nl/people/StefanKlein


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