elastixLogo.gif Model Zoo

A Model Zoo for parameter files used for image registration with Elastix, SimpleElastix or ITKElastix in various domains. Parameter files can be uploaded via the GitHub repository.

Par0001

interpatient; affine + B-spline transformation; mutual information

Prostate 3D MRI
Par0002

interpatient; several transformation models; localised mutual information

Brain 3D PET MRI
Par0005

intrapatient; rigid + B-spline transformation; multi-feature α-mutual information

Cervix 3D MRI
Par0009

interpatient; B-spline transformation; mutual information

Brain 3D MRI
Par0010

interpatient; affine + B-spline transformation; mutual information

Brain 3D MRI
Par0012

motion estimation; (cyclic) B-spline transformation; variance over last dimension

Carotid Cardiac Chest/Lung 3D 4D CT MRI Ultrasound
Par0017

intrapatient; rigid; localized mutual information

Knee 3D MRI
Par0018

interpatient; several transformation models; mutual information based similarity metrics

Carotid 2D 3D MRI
Par0020

intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty

Brain 3D MRI
Par0021

Registration optimisation for subject-FA images to FA template, multiple data sources

Brain MRI
Par0022

intrapatient; rigid + B-spline transformation; statistical shape regularization

Cervix 3D MRI
Par0023

intrapatient; rigid + B-spline transformation; localized mutual information combined with bending energy penalty

Head & Neck CT MRI PET
Par0024

interpatient; rigid + B-spline transformation; missing structure penalty

Cervix 3D MRI
Par0025

intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty

Brain 3D MRI
Par0026

intra-subject, longitudinal data; rigid + affine + B-spline transformation

Brain 3D MRI
Par0027

intra patient; rigid + B-spline transformation; mutual information, multi parametric mutual information

Head & Neck CT MRI PET
Par0029

intra patient; B-spline transformation; mutual information

Abdomen 3D MRI
Par0030

inter patient; Affine + B-spline transformation; normalized cross correlation. intra patient; Rigid transformation; mutual information

MRI
Par0032

intrapatient; rigid + B-spline transformation; mutual information

3D MRI
Par0033

inter-subject; rigid + affine + B-spline transformation; mutual information metric with a transform bending energy penalty

Brain 3D MRI
Par0034

inter-subject; rigid + affine + B-spline transformation; advanced normalized correlation + mutual information metric with a transform bending energy penalty

Brain MRI
Par0035

intra-subject, inter-subject; mono-modal and multi-modal; rigid, affine and B-spline transformations; mean square difference, normalized correlation, mutual information

Brain Abdomen Chest/Lung 3D 4D CT Ultrasound MRI
Par0036

intra-subject, inter-station; affine; normalized correlation

2D MRI
Par0038

intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty

Brain 3D MRI
Par0039

intra-subject; affine or B-spline transformation; groupwise registration; PCA metrics

Brain Carotid Abdomen 2D 3D 4D MRI
Par0040

intra-subject; affine transformation, mutual information metric

3D MRI
Par0041

inter-subject; similarity + B-spline transformation, advanced normalized correlation metric

MRI
Par0042

inter-subject; rigid + B-spline transformation, advanced normalized correlation metric

MRI
Par0043

intra-subject; multi-resolution (4), rigid, Mutual Information metric (Mattes) with Adaptive Stochastic Gradient Descent optimizer

Prostate Pelvis 3D CT MRI
Par0047

intra-subject; B-spline transformation; groupwise registration; PCA metric

Abdomen Liver 4D MRI
Par0048

intra-subject; B-spline transformation; Mattes mutual information

3D MRI
Par0050

intra-subject; affine transformation, mutual information metric

3D MRI
Par0051

inter-subject; similarity + B-spline transformation, advanced normalized correlation metric

MRI
Par0052

inter-subject; Longitudinal Data, affine + B-spline transformation

3D MRI
Par0055

intra-subject cine-MRI motion; rigid transformation

Prostate 3D MRI
Par0057

intra-subject; Rigid transformation; B-spline transformation

Liver 4D MRI
Par0059

Intrapatient, B-spline transformation, mutual information, rigidity penalty

Pelvis 3D CT MRI
Par0060

Intapatient, rigid+ affine+ b-spline transformation, mutual information

Abdomen Head & Neck 2D MRI
Par0061

Intrapatient, rigid transformation

Pelvis 3D MRI
Par0062

This multi-step registration is used to register follow-up images to the reference MRI. Patients are...

MRI
Par0064

interpatient; affine transform; mutual information

Brain 3D MRI
Name Image Properties Description Paper
Par0001 Prostate 3D MRI interpatient; affine + B-spline transformation; mutual information S. Klein, M. Staring, K. Murphy, M.A. Viergever, 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, 2010.
Par0002 Brain 3D PET MRI interpatient; several transformation models; localised mutual information S. Klein, M. Staring, K. Murphy, M.A. Viergever, 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, 2010.
Par0005 Cervix 3D MRI intrapatient; rigid + B-spline transformation; multi-feature α-mutual information 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.
Par0009 Brain 3D MRI interpatient; B-spline transformation; mutual information Artaechevarria X, Munoz-Barrutia A, Ortiz-de-Solorzano C., "Combination strategies in multi-atlas image segmentation: application to brain MR data," IEEE Trans Med Imaging. 2009 Aug;28(8):1266-77.
Par0010 Brain 3D MRI interpatient; affine + B-spline transformation; mutual information S. Klein, M. Loog, F. van der Lijn, T. den Heijer, A. Hammers, M. de Bruijne, A. van der Lugt, R.P.W. Duin, M.M.B. Breteler and W.J. Niessen, Early diagnosis of dementia based on intersubject whole-brain dissimilarities, Proceedings of IEEE International Symposium on Biomedical Imaging: from Nano to Macro, 2010.
Par0012 Carotid Cardiac Chest/Lung 3D 4D CT MRI Ultrasound motion estimation; (cyclic) B-spline transformation; variance over last dimension Nonrigid registration of dynamic medical imaging data using nD+t B-splines and a groupwise optimization approach, C.T. Metz, S. Klein, M. Schaap, T. van Walsum and W.J. Niessen, Medical Image Analysis, in press](http://dx.doi.org/10.1016/j.media.2010.10.003)
Par0017 Knee 3D MRI intrapatient; rigid; localized mutual information E.E. Bron, J. van Tiel, H. Smit, D.H.J. Poot, W.J. Niessen, G. P. Krestin, H. Weinans, E. Oei, G. Kotek and S. Klein, Image registration improves human knee cartilage T1 mapping with delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), European Radiology, in press_
Par0018 Carotid 2D 3D MRI interpatient; several transformation models; mutual information based similarity metrics Automatic Registration of Multispectral MR Vessel Wall Images of the Carotid Artery R. van 't Klooster, M. Staring, S. Klein, R.M. Kwee, M.E. Kooi, J. H. C. Reiber, B.P.F. Lelieveldt and R.J. van der Geest, International Society for Magnetic Resonance in Medicine, 2012
Par0020 Brain 3D MRI intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty A. Khmelinskii, L. Mengler, P. Kitslaar, M. Staring, M. Hoehn and B.P.F. Lelieveldt, "A visualization platform for high-throughput, follow-up, co-registered multi-contrast MRI rat brain data," SPIE Medical Imaging: Biomedical Applications in Molecular, Structural, and Functional Imaging, Proceedings of SPIE, vol. 8672, pp. 86721W–86721W-7, February 2013](http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1674633)
Par0021 Brain MRI Registration optimisation for subject-FA images to FA template, multiple data sources M. de Groot, M.W. Vernooij, M.A. Ikram, F Vos, S.M. Smith, W.J. Niessen and J. Andersson, Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration., NeuroImage 76, 400-411
Par0022 Cervix 3D MRI intrapatient; rigid + B-spline transformation; statistical shape regularization F.F. Berendsen et al., Free-form image registration regularized by a statistical shape model: application to organ segmentation in cervical MR, Comput. Vis. Image Understand. (2013),
Par0023 Head & Neck CT MRI PET intrapatient; rigid + B-spline transformation; localized mutual information combined with bending energy penalty S. Leibfarth , D. Mönnich, S. Welz, C. Siegel, N. Schwenzer, H. Schmidt, D. Zips, D. Thorwarth, A strategy for multimodal deformable image registration to integrate PET/MR into radiotherapy treatment planning, Acta Oncologica 52, 1353-1359 (2013)
Par0024 Cervix 3D MRI interpatient; rigid + B-spline transformation; missing structure penalty F.F. Berendsen et al., Registration of structurally dissimilar images in MRI-based brachytherapy, Phys. Med. Biol. 59 (2014) 4033-4045.
Par0025 Brain 3D MRI intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty L. Hammelrath, S. Škokić, A. Khmelinski, A. Hess, N. van der Knaap, M. Staring, B.P.F. Lelieveldt, D. Wiedermann, M. Hoehn, "Morphological maturation of the mouse brain: an _in vivo_ MRI and histology investigation," NeuroImage, 2015](http://www.sciencedirect.com/science/article/pii/S1053811915009039)
Par0026 Brain 3D MRI intra-subject, longitudinal data; rigid + affine + B-spline transformation L. Hammelrath, A. Khmelinskii, C. Po, E. Pracht, H. Endepols, H. Backes, C. Schäfer, M. Staring, B.P.F. Lelieveldt and M. Hoehn, "," _in preparation_, 2016
Par0027 Head & Neck CT MRI PET intra patient; rigid + B-spline transformation; mutual information, multi parametric mutual information V. Fortunati, R.F. Verhaart, F. Angeloni, A. van der Lugt, W.J. Niessen, J.F. Veenland, M.M. Paulides and T. van Walsum, Feasibility of Multimodal Deformable Registration for Head and Neck Tumor Treatment Planning, Int. J. Radiation Oncology Biology and physics 90, 85-93 (2014)
Par0029 Abdomen 3D MRI intra patient; B-spline transformation; mutual information J.-M. Guyader, L. Bernardin, N. H. M. Douglas, D. H. J. Poot, W. J. Niessen, S. Klein, Influence of image registration on apparent diffusion coefficient images computed from free-breathing diffusion MR images of the abdomen, Journal of Magnetic Resonance in Medicine, 2014
Par0030 MRI inter patient; Affine + B-spline transformation; normalized cross correlation. intra patient; Rigid transformation; mutual information : https://github.com/SuperElastix/ElastixModelZoo/raw/master/models/Par0030/Post11.png
Par0032 3D MRI intrapatient; rigid + B-spline transformation; mutual information A. Gubern-Mérida; R. Marti; J. Melendez; J. Hauth; R. Mann; N. Karssemeijer and B. Platel. "Automated localization of breast cancer in DCE-MRI", Medical Image Analysis 2015;20:265-274.
Par0033 Brain 3D MRI inter-subject; rigid + affine + B-spline transformation; mutual information metric with a transform bending energy penalty D.I. Bink, K. Ritz, C. Mackaaij, A. Khmelinskii, O.J. de Boer, L.M. Gierman, J.C. Sluimer, L. van der Weerd, M.J.A.P. Daemen, "Neuropathology in mouse models for atherosclerosis," _Submitted_ 2016]
Par0034 Brain MRI inter-subject; rigid + affine + B-spline transformation; advanced normalized correlation + mutual information metric with a transform bending energy penalty D.I. Bink _et al.,_ "," _in preparation_ 2016]
Par0035 Brain Abdomen Chest/Lung 3D 4D CT Ultrasound MRI intra-subject, inter-subject; mono-modal and multi-modal; rigid, affine and B-spline transformations; mean square difference, normalized correlation, mutual information 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, in press.
Par0036 2D MRI intra-subject, inter-station; affine; normalized correlation O. Dzyubachyk, M. Staring, M. Reijnierse, B.P.F. Lelieveldt, and R.J. van der Geest. "Inter-Station Intensity Standardization for Whole-Body MR Data", Magnetic Resonance in Medicine 2017;77(1):422–433.](https://www.frontiersin.org/articles/10.3389/fninf.2017.00003/full)
Par0038 Brain 3D MRI intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty I.A. Mulder*, A. Khmelinskii*, O. Dzyubachyk*, N. Rieff, S. de Jong, M.J.H. Wermer, M. Hoehn, B.P.F. Lelieveldt, A.M.J.M. van den Maagdenberg, "Automated ischemic lesion segmentation in MRI mouse brain data after transient middle cerebral artery occlusion," Front. Neuroinform, Vol. 11, Issue 3, January 2017](https://www.frontiersin.org/articles/10.3389/fninf.2017.00003/full)
Par0039 Brain Carotid Abdomen 2D 3D 4D MRI intra-subject; affine or B-spline transformation; groupwise registration; PCA metrics /j.media.2015.12.004 PCA-based groupwise image registration for quantitative MRI, W. Huizinga, D.H.J. Poot, J.-M. Guyader, R. Klaassen, B.F. Coolen, M. van Kranenburg, R.J.M. van Geunse, A. Uitterdijk, M. Polfliet, J. Vandemeulebroucke, A. Leemans, W.J. Niessena, S. Klein, Medical Image Analysis, in press]
Par0040 3D MRI intra-subject; affine transformation, mutual information metric None
Par0041 MRI inter-subject; similarity + B-spline transformation, advanced normalized correlation metric None
Par0042 MRI inter-subject; rigid + B-spline transformation, advanced normalized correlation metric None
Par0043 Prostate Pelvis 3D CT MRI intra-subject; multi-resolution (4), rigid, Mutual Information metric (Mattes) with Adaptive Stochastic Gradient Descent optimizer Maspero M, et al. (2017), Quantification of confounding factors in MRI-based dose calculations as applied to prostate IMRT. Phys Med Biol. 62(3)
Par0047 Abdomen Liver 4D MRI intra-subject; B-spline transformation; groupwise registration; PCA metric M. J. A. Jansen, H. J. Kuijf, W. B. Veldhuis, F. J. Wessels, M. van Leeuwen, and J. P. W. Pluim, " Evaluation of motion correction for clinical dynamic contrast enhanced MRI of the liver," Phys. Med. Biol., 62(19), pp. 7556–7568, 2017.
Par0048 3D MRI intra-subject; B-spline transformation; Mattes mutual information G. Abreu-Vieira*, J. Burakiewicz*, L.G.M. Janssen, K.J. Nahon, M.R. Boon, O. Dzyubachyk, A.G. Webb, H.E. Kan, P.C.N. Rensen. "Human brown adipose tissue lipid mapping by MRI and its heterogenic changes in volume, mass and energy content after cold exposure"
Par0050 3D MRI intra-subject; affine transformation, mutual information metric None
Par0051 MRI inter-subject; similarity + B-spline transformation, advanced normalized correlation metric None
Par0052 3D MRI inter-subject; Longitudinal Data, affine + B-spline transformation Mehrabian H., Lu Y., Richmond L., Martel, A.L., [Deformable registration for longitudinal breast MRI screening][2], Journal of Digital Imaging (2018). doi.org/10.1007/s10278-018-0063-1
Par0055 Prostate 3D MRI intra-subject cine-MRI motion; rigid transformation de Muinck Keizer DM, Kerkmeijer LG, Maspero M, Andreychenko A, van Zyp JV, Van den Berg CA, Raaymakers BW, Lagendijk JJ, de Boer JC. Soft-tissue prostate intrafraction motion tracking in 3D cine-MR for MR-guided radiotherapy. Physics in Medicine & Biology. 2019 Dec 5;64(23):235008. doi:[https://doi.org/10.1088/1361-6560/ab5539](https://doi.org/10.1088/1361-6560/ab5539).
Par0057 Liver 4D MRI intra-subject; Rigid transformation; B-spline transformation Jansen et al. (2019) Liver segmentation and metastases detection in MR images using convolutional neural networks (submitted)
Par0059 Pelvis 3D CT MRI Intrapatient, B-spline transformation, mutual information, rigidity penalty Florkow et al. (2019), Deep learning-based MR-to-CT synthesis: the influence of varying gradient echo-based MR images as input channels, under submission
Par0060 Abdomen Head & Neck 2D MRI Intapatient, rigid+ affine+ b-spline transformation, mutual information Terpstra ML, Maspero M, D'Agata F, Stemkens B, Intven MP, Lagendijk JJ, Van den Berg CA, Tijssen RH. Deep learning-based image reconstruction and motion estimation from undersampled radial k-space for real-time MRI-guided radiotherapy. Physics in Medicine & Biology. 2020 July 30; 66(15). doi:[https://doi.org/10.1088/1361-6560/ab9358](https://doi.org/10.1088/1361-6560/ab9358).
Par0061 Pelvis 3D MRI Intrapatient, rigid transformation Werensteijn-Honingh et al. (2020), Impact of a vacuum cushion on intrafraction motion during online adaptive MR-guided SBRT, submitted.
Par0062 MRI This multi-step registration is used to register follow-up images to the reference MRI. Patients are... None
Par0064 Brain 3D MRI interpatient; affine transform; mutual information Paper to be published, reference will be added at a later time.

© 2020 Viktor van der Valk