This parameter file database entry contains "default" parameter files. These are intended for starting elastix users, and should give reasonable results in many applications. The elastix example (version 4.3 or higher), which can be downloaded from the website contains the same parameter files, together with a test pair of images and an example script that calls elastix.
''Needless to say, it is virtually impossible to come up with default parameter values that give satisfactory results for every application. The parameter files provided here should rather be considered as a starting point.''
For parameter files see the Elastix Model Zoo repository on GitHub.
elastix version: 4.3 and higher.
Example command line call:
elastix -f fixed.mhd -m moving.mhd -p parameters_Rigid.txt -p parameters_BSpline.txt -out outputdir
Up to elastix 4.5 the image dimensions had to be specified by the user.
(FixedImageDimension 2) -> (FixedImageDimension 3)
(MovingImageDimension 2) -> (MovingImageDimension 3)
From elastix 4.6, this is not necessary anymore.
NB2: The files are saved in DOS text format. In order to use them on a Linux-based system, use the dos2unix tool to convert them to unix text format.
See the elastix manual for an extensive introduction to elastix and explanation of many parameters. If you have any questions, please subscribe to the elastix mailing list and post your question there. We (the authors of elastix) are happy to answer any questions. Please do read the FAQ though ;)
A static jupyter notebook example for usage in python can be found here
© 2020 Viktor van der Valk