[Elastix] Mimicking Fiji's Register_Virtual_Stack
s.klein at erasmusmc.nl
Thu Aug 4 11:44:20 CEST 2016
1) The old post you refer to is still up-to-date. It seems a sensible
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.
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
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