intra-mouse; B-spline transformation; combination of normalized correlation and the Euclidean distance metric
3D registration was performed using the following:
Shown are (left to right) 1) Moving image 2) Fixed image 3) Registration with NCC only and 4) Registration with NCC and EDM. The arrows indicate where the registration with the NCC only fails.
For parameter files see the Elastix Model Zoo repository on GitHub.
elastix
version: 4.403
Parameter file for the NCC B-Spline registration, initialized by a similarity registration, is indicated with '.NCC.txt'.
Command line call:
elastix -f fixed_image.mhd -m moving_image.mhd -p parameters.similarity.txt -p parameters.NCC.txt -out resultDir
Parameter file for the NCC plus EDM B-Spline registration, initialized by a similarity registration, is indicated with 'NCC_EDM.txt'
Command line call:
elastix -f fixed_image.mhd -m moving_image.mhd -fp fixedPointSet.txt -mp movingPointSet.txt -p parameters.similarity.txt
-p parameters.NCC_EDM.txt -out resultDir
Baiker (2011), Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice [1]
[1] Baiker, M.; Milles, J.; Dijkstra, J.; Henning, T.; Weber, A.; Que, I.; Kaijzel, E.; Löwik, C.; Reiber, J. & Lelieveldt, B.: Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data. Medical Image Analysis, 2010, 14, 723-737
[2] Baiker, M.; Staring, M.; Löwik, C. W. G. M.; Reiber, J. H. C. & Lelieveldt, B. P. F.: Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2011, Springer, 2011
© 2020 Viktor van der Valk