[Elastix] question on Elastix

Chris Bouwman Chris.Bouwman at pie.nl
Mon Apr 8 10:05:41 CEST 2013

Hello Stefan, Dan,

Here a small guideline to generate and use elastix dll:

generate project using CMAKE
To Generate the dll, get the latest files from the trunkpublic.
Generate the project using CMake (remove checkmark from setting ELASTIX BUILD EXECUTABLE).

The following types are used on the interface:
Note that these image must be passed to the dll as a itk::DataObject::Pointer, this can be reached by calling GetPointer() on the itk::image.

note that the pixel type of mask images must be unsigned char!

The result image pixeltype must be the type as specified in the registration parameters (parameter "ResultImagePixelType"). Note that for now elastix can only handle short and unsigned short pixel types.

registration parameters:
Are passed to the dll as a ParameterMapType being a std::map<> containing a string holding the Parametername and a vector<std::string> containing one or more parameter values.

For now the dll can only generate a result image. I also added functionality that enables the user to get the applied transformation.
Furthermore I adapted the code to generate a transformix dll.
However, I have not committed these changes to the trunckpublic so far.

Dan, I do not know what Blitz++ is, so I don't now if that works.

Chris Bouwman.

From: Dan Xu [mailto:danxu2008 at gmail.com]
Sent: donderdag 4 april 2013 22:03
To: S. Klein
Cc: Elastix; Chris Bouwman
Subject: Re: question on Elastix

Hi Stefan
Thank you very much for the information.

Could you shed some light on how to call/modify Elastix functions so that it accepts 3D image data (e.g., multidimensional array in Blitz++) in memory as input?

Thank you,

On Thu, Apr 4, 2013 at 9:45 AM, S. Klein <s.klein at erasmusmc.nl<mailto:s.klein at erasmusmc.nl>> wrote:
Hi Dan,
Thanks for your interest in elastix. I forward your mail to the mailing list. You can subscribe to this via the website.
Chris Bouwman (cc, but I think he's on the list as well) has developed a library interface for elastix. It's still work in progress, but you could already give it a try.
Chris, could you give a few hints on how to start?

On 03/04/2013 20:31, Dan Xu wrote:
Dear Stefan,

I'm trying to use your wonderfully put-together Elastix for some image volume registration. The command line based registration works fine. What I'd really like to do is to call your functions from my main c++ code (where tons of other functionalities, including image reconstruction, exist).

Could you give me some suggestions on how I should call/modify your functions so that it accepts 3D image data in memory as input, instead of from files? I'd also like to supply the parameters through input arguments, rather than from a file if possible.

The 3D image data format I use is the multidimensional array format in Blitz.

Thanks a lot,


Stefan Klein

+31 10 7043049<tel:%2B31%2010%207043049>


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