How to cite elastix (components)

Main citations

If you use elastix anywhere we would appreciate if you cite the following articles:

• S. Klein, M. Staring, K. Murphy, M.A. Viergever and J.P.W. Pluim, "elastix: a toolbox for intensity based medical image registration," IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010. download doi citations

• D.P. Shamonin, E.E. Bron, B.P.F. Lelieveldt, M. Smits, S. Klein and M. Staring, "Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer’s Disease", Frontiers in Neuroinformatics, vol. 7, no. 50, pp. 1-15, January 2014. download doi citations

The reference for SimpleElastix is

• K. Marstal, F. Berendsen, M. Staring and S. Klein, "SimpleElastix: A user-friendly, multi-lingual library for medical image registration," International Workshop on Biomedical Image Registration (WBIR), IEEE Conference on Computer Vision and Pattern Recognition Workshops, pp. 574 - 582, July 2016. download doi citations

elastix components

Many of the elastix components were published in scientific journals. If you are using them, here you can find the appropriate citation:

elastix setting	Citation
The stochastic gradient descent optimisation routine
(Optimizer "StandardGradientDescent") (ImageSampler "Random") or (ImageSampler "RandomSparseMask") or (ImageSampler "RandomCoordinate") (NewSamplesEveryIteration "true") See also the doxygen documentation here and here.	Stefan Klein, Marius Staring and Josien P.W. Pluim, "Evaluation of Optimization Methods for Nonrigid Medical Image Registration using Mutual Information and B-splines," IEEE Transactions on Image Processing, vol. 16, no. 12, pp. 2879 - 2890, December 2007. download
The rigidity penalty term
(Metric "SimilariyMetricOfChoice" "TransformRigidityPenalty") See also the doxygen documentation here and here.	Marius Staring, Stefan Klein and Josien P.W. Pluim, "A Rigidity Penalty Term for Nonrigid Registration," Medical Physics, vol. 34, no. 11, pp. 4098 - 4108, November 2007. download
Higher order mutual information, implemented with k-nearest neighbour graphs
(Metric "KNNGraphAlphaMutualInformation") (Registration "MultiResolutionRegistrationWithFeatures") (ImageSampler "MultiInputRandomCoordinate") See also the doxygen documentation here and here.	M. Staring, U.A. van der Heide, S. Klein, M.A. Viergever and J.P.W. Pluim, "Registration of Cervical MRI Using Multifeature Mutual Information," IEEE Transactions on Medical Imaging, vol. 28, no. 9, pp. 1412 - 1421, September 2009. download
The adaptive stochastic gradient descent (ASGD) optimisation method
(Optimizer "AdaptiveStochasticGradientDescent") (ImageSampler "Random") or (ImageSampler "RandomSparseMask") or (ImageSampler "RandomCoordinate") (NewSamplesEveryIteration "true") See also the doxygen documentation here and here.	S. Klein, J.P.W. Pluim, and M. Staring, M.A. Viergever, "Adaptive stochastic gradient descent optimisation for image registration," International Journal of Computer Vision, vol. 81, no. 3, pp. 227-239, 2009. download
The cyclic version of the BSplineTransform, the VarianceOverLastDimensionMetric or the BSplineStackTransform
(Transform "BSplineTransform") with (UseCyclicTransform "true") or (Transform "BSplineStackTransform") or (Metric "VarianceOverLastDimensionMetric") See also the doxygen documentation for the BSplineTransform, BSplineStackTransform and VarianceOverLastDimensionMetric.	C.T. Metz, S. Klein, M. Schaap, T. van Walsum and W.J. Niessen, "Nonrigid registration of dynamic medical imaging data using nD+t B-splines and a groupwise optimization approach," Medical Image Analysis, vol. 15, no. 2, pp. 238 - 249, 2011. download
The corresponding point Euclidean distance metric
(Metric "CorrespondingPointsEuclideanDistanceMetric") See also the doxygen documentation here and here.	M. Baiker, M. Staring, C.W.G.M. Löwik, J.H.C. Reiber and B.P.F. Lelieveldt, "Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice," MICCAI, Lecture Notes in Computer Science, vol. 6892, pp. 516 - 523, 2011. download
The 2D-3D registration framework
(Metric "GradientDifference") or (Metric "NormalizedGradientCorrelation") or (Metric "PatternIntensity") or (ResampleInterpolator "RayCastResampleInterpolator") or (Interpolator "RayCastInterpolator") or (Optimizer "Powell") or (Optimizer "Simplex") or See also the doxygen documentation for GradientDifference, NormalizedGradientCorrelation, PatternIntensity, RayCastResampleInterpolator, RayCastInterpolator, Powell and Simplex.	I.M.J. van der Bom, "2D-3D Image Registration in Diagnostic and Interventional X-ray Imaging", Utrecht University, The Netherlands, December 2010. download I.M.J. van der Bom, S. Klein, M. Staring, R. Homan, L.W. Bartels, J.P.W. Pluim, "Evaluation of optimization methods for intensity-based 2D-3D registration in X-ray guided interventions", in: SPIE Medical Imaging: Image Processing, SPIE Press, vol. 7962, pp. 796223-1 - 796223-15, 2011. download
Adaptation of the B-spline transform for sliding objects
(Transform "MultiBSplineTransformWithNormal") See also the doxygen documentation here and here.	V. Delmon, S. Rit, R. Pinho and D. Sarrut, "Direction dependent B-splines decomposition for the registration of sliding objects", Workshop on Pulmonary Image Analysis, 2011. download V. Delmon, S. Rit, R. Pinho and D. Sarrut, "Registration of sliding objects using direction dependent B-splines decomposition", Physics in Medicine and Biology, vol. 58, no. 5, pp. 1303 - 1314, 2013. download
Regularization metric based on statistical shape
(Metric "StatisticalShapePenalty") See also the doxygen documentation here and here.	F.F. Berendsen, U.A. van der Heide, T.R. Langerak, A.N.T.J. Kotte and J.P.W. Pluim, "Free-form image registration regularized by a statistical shape model: application to organ segmentation in cervical MR", vol. 117, no. 9, pp. 1119 - 1127, 2013. download
Fast automatic step size estimation for the ASGD optimizer
(Optimizer "AdaptiveStochasticGradientDescent") (ASGDParameterEstimationMethod "DisplacementDistribution") See also the doxygen documentation here and here.	Y. Qiao, B. van Lew, B.P.F. Lelieveldt and M. Staring, "Fast Automatic Step Size Estimation for Gradient Descent Optimization of Image Registration", IEEE Transactions on Medical Imaging, vol. 35, no. 2, pp. 391 - 403, 2016. download
OpenCL-based components for accelerated registration
(Resampler "OpenCLResampler") See also the doxygen documentation here and here. And also: (FixedImagePyramid "OpenCLFixedGenericImagePyramid") (MovingImagePyramid "OpenCLMovingGenericImagePyramid")	D.P. Shamonin, E.E. Bron, B.P.F. Lelieveldt, M. Smits, S. Klein and M. Staring, "Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer's Disease," Frontiers in Neuroinformatics, vol. 7, no. 50, pp. 1-15, January 2014. download
Mass-preserving Mean Square Difference metric
(Metric "SumSquaredTissueVolumeDifference") This code was contributed by Geoffrey D. Hugo and his group.	V. Gorbunova, J. Sporring, P. Lo, M. Loeve, H.A. Tiddens, M. Nielsen and M. de Bruijne, "Mass preserving image registration for lung CT", Medical Image Analysis, vol. 16, no. 4, pp. 786 - 795, 2012. download Y. Yin, E.A. Hoffman and C.L. Lin, "Mass preserving nonrigid registration of CT lung images using cubic B-spline", Medical Physics, vol. 36, no. 9, pp. 4213 - 4222, 2009. download
Fast recursive implementation of the B-spline transform
(Transform "RecursiveBSplineTransform")	W. Huizinga, S. Klein and D.H.J. Poot, "Fast Multidimensional B-spline Interpolation Using Template Metaprogramming," 6th International Workshop Biomedical Image Registration (WBIR), pp. 11-20, 2014. download
The preconditioned adaptive stochastic gradient descent method (PASGD)
(Optimizer "PreconditionedStochasticGradientDescent") The AdaGrad optimizer was also implemented as part of this paper.	Y. Qiao, B.P.F. Lelieveldt, and M. Staring, "An efficient preconditioner for stochastic gradient descent optimization of image registration", IEEE Transactions on Medical Imaging, vol. , no. , pp. , 2019. download