Parameter file database

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This is the main page of the elastix parameter file database. The parameter file database is a collection of elastix parameter files. Each parameter file is accompanied by a description of the data/application for which the parameter file was successfully used. New elastix users may find here many examples of usage. Scroll through the list below and find the data/application most similar to your own!

All elastix users are encouraged to add their own parameter files!

An important aspect of science is reproducibility. When you have successfully used elastix for a scientific publication, please post the parameter files here. In this way, readers will be able to reproduce your results more easily.

When adding a database entry, please try to adhere to the layout/formatting of other database entries, to maintain uniformity.

The Database

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Link Image modality Image content Short description First author (year) - title of publication [optional]
default0 all all "default" parameter files for starting elastix users
par0000 3D MR T1, monomodal brain interpatient; affine + B-spline transformation; mutual information van der Lijn (2009) - Cerebellum Segmentation in MRI Using Atlas Registration and Local Multi-Scale Image Descriptors
par0001 3D MR BFFE, monomodal prostate interpatient; several transformation models; localised mutual information Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration
par0002 3D MR T1 & PET brain intrapatient; translation; mutual information Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration
par0003 3D CT, monomodal lung interpatient; affine + B-spline transformation; mutual information Klein & Staring (2010) - elastix: a toolbox for intensity-based medical image registration
par0004 3D CT, monomodal lung intrapatient; rigid + B-spline transformation; mutual information Staring (2007) - A Rigidity Penalty Term for Nonrigid Registration
par0005 3D MR T2, monomodal cervix intrapatient; rigid + B-spline transformation; multi-feature α-mutual information Staring (2009) - Registration of Cervical MRI Using Multifeature Mutual Information
par0006 3D MR T2*, histology tumor rigid + B-spline transformation; multi-feature α-mutual information Alic (2011) - Facilitating tumor functional assessment by spatially relating 3D tumor histology and in vivo MRI: Image registration approach
par0007 4D CT, monomodal lung intrapatient; B-spline transformation; mutual information Ding (2010) - 4DCT-Based Measurement of Radiation Induced Changes in Pulmonary Function
par0008 3D CT, monomodal lung intrapatient; B-spline transformation; mutual information Murphy (2008) - Semi-Automatic Reference Standard Construction for Quantitative Evaluation of Lung CT Registration
par0009 3D MRI, monomodal brain interpatient; B-spline transformation; mutual information Artaechevarria (2009) - Combination strategies in multi-atlas image segmentation: application to brain MR data
par0010 3D MR HASTE, monomodal brain interpatient; affine + B-spline transformation; mutual information Klein (2010) - Early diagnosis of dementia based on intersubject whole-brain dissimilarities
par0011 3D CT, monomodal lung intrapatient (sometimes intra-sheep); B-spline transformation; normalized correlation Staring (2010), Pulmonary Image Registration With elastix Using a Standard Intensity-Based Algorithm
par0012 4D CT(A), 3D MR, 3D US, 3D synthetic, monomodal heart, lung, carotid motion estimation; (cyclic) B-spline transformation; variance over last dimension Metz (2011), Nonrigid registration of dynamic medical imaging data using nD+t B-splines and a groupwise optimization approach
par0013 2D x-ray - 3D CT cerebral registration of interventional x-ray data to 3D CT for motion estimation, patient positioning or image guidance van der Bom (2011), Evaluation of optimization methods for intensity-based 2D-3D registration in x-ray guided interventions
par0014 3D microCT whole-body mouse intra-mouse; B-spline transformation; combination of normalized correlation and the Euclidean distance metric Baiker (2011), Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice
par0015 3D CT, monomodal lung intrapatient; B-spline transformation; several similarity metrics Staring (2013), Towards Local Progression Estimation of Pulmonary Emphysema using CT
par0016 3D CT, monomodal lung intrapatient; Multi B-spline transformation; sliding motion Delmon (2011), Direction dependent B-splines decomposition for the registration of sliding objects
par0017 3D MR, monomodal knee cartilage intrapatient; rigid; localized mutual information Bron (2013) - Image registration improves human knee cartilage T1 mapping with delayed Gadolinium Enhanced MRI of Cartilage (dGEMRIC)
par0018 3D MR, multi sequence carotid artery interpatient; several transformation models; mutual information based similarity metrics van 't Klooster - Automated Registration of Multispectral MR Vessel Wall Images of the Carotid Artery
par0019 3D CT, monomodal head and neck inter patient; rigid and B-spline transformation, advanced mean square and normalized correlation metrics Fortunati (2013) - Atlas based segmentation for hyperthermia treatment planning
par0020 3D MR, multi-contrast rat brain intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty Khmelinskii (2013) - A visualization platform for high-throughput, follow-up, co-registered multi-contrast MRI rat brain data

Mengler (2014) - Brain maturation of the adolescent rat cortex and striatum: changes in volume and myelination

par0021 DT-MRI brain Registration optimisation for subject-FA images to FA template, multiple data sources De Groot (2013), Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration
par0022 3D MR T2, monomodal cervix intrapatient; rigid + B-spline transformation; statistical shape regularization Berendsen (2013), Free-form image registration regularized by a statistical shape model: application to organ segmentation in cervical MR
par0023 3D CT, 3D MR, multimodal head and neck intrapatient; rigid + B-spline transformation; localized mutual information combined with bending energy penalty Leibfarth (2013), A strategy for multimodal deformable image registration to integrate PET/MR into radiotherapy treatment planning
par0024 3D MR T2, monomodal cervix interpatient; rigid + B-spline transformation; missing structure penalty Berendsen (2014), Registration of structurally dissimilar images in MRI-based brachytherapy
par0025 3D MR, multi-contrast mouse brain intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty Hammelrath (2015) - Morphological maturation of the mouse brain: an in vivo MRI and histology investigation
par0026 3D MR, multi-contrast rat brain intra-subject, longitudinal data; rigid + affine + B-spline transformation Hammelrath (2016)
par0027 3D CT, 3D MR, multimodal, multi sequence head and neck intra patient; rigid + B-spline transformation; mutual information, multi parametric mutual information Fortunati (2014), Feasibility of Multimodal Deformable Registration for Head and Neck Tumor Treatment Planning
par0028 3D CT, monomodal head and neck intra patient; rigid + B-spline transformation; several B-pline knot spacings; synthesized head and neck phantoms Brouwer (2014), The effects of CT image characteristics and knot spacing on the spatial accuracy of B-spline deformable image registration in the head and neck geometry
par0029 3D diffusion-weighted MR images (DW-MRI) abdomen intra patient; B-spline transformation; mutual information Guyader (2014) - Influence of image registration on apparent diffusion coefficient images computed from free-breathing diffusion MR images of the abdomen
par0030 3D T1 and T1 fat-suppressed gadolinium-enhanced extremity MR images wrist inter patient; Affine + B-spline transformation; normalized cross correlation. intra patient; Rigid transformation; mutual information Roex - MSc thesis: Early Detection of Rheumatoid Arthritis using extremity MRI: Quantification of Bone Marrow Edema in the Carpal bones
par0031 3D CT, monomodal thorax intrapatient; regional-independent B-spline transformation; sliding surface penalty Berendsen (2014), Registration of organs with sliding interfaces and changing topologies
par0032 3D DCE-MRI breast intrapatient; rigid + B-spline transformation; mutual information Gubern-Mérida (2015), Automated localization of breast cancer in DCE-MRI
par0033 3D MR mouse brain inter-subject; rigid + affine + B-spline transformation; mutual information metric with a transform bending energy penalty Bink (2016), Kogelman (2016)
par0034 2D CBF MR mouse brain inter-subject; rigid + affine + B-spline transformation; advanced normalized correlation + mutual information metric with a transform bending energy penalty Bink (2016)
par0035 CT, MR, ultrasound brain, lung, abdomen intra-subject, inter-subject; mono-modal and multi-modal; rigid, affine and B-spline transformations; mean square difference, normalized correlation, mutual information Qiao (2015), Fast Automatic Step Size Estimation for Gradient Descent Optimization of Image Registration
par0036 MRI joint histograms whole-body intra-subject, inter-station; affine; normalized correlation Dzyubachyk (2015)
par0037 DTS lung intra-subject; translational registration; mutual information You (2015)
par0038 MRI mouse brain stroke intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty Mulder, Khmelinskii, Dzyubachyk (2016)
par0039 quantitative MRI porcine heart, abdomen, carotid, brain intra-subject; affine or B-spline transformation; groupwise registration; PCA metrics Huizinga (2016), PCA-based groupwise image registration for quantitative MRI
par0040 extremity MRI wrist intra-subject; affine transformation, mutual information metric Aizenberg (2016)
par0041 extremity MRI wrist inter-subject; similarity + B-spline transformation, advanced normalized correlation metric Aizenberg (2016)
par0042 MRI spine inter-subject; rigid + B-spline transformation, advanced normalized correlation metric Aizenberg (2016)
par0043 CT/ MR-based pseudo-CT pelvis (prostate) intra-subject; multi-resolution (4), rigid + B-spline transformation, 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)
par0044 3D CT, multi-contrast cardiac intra-subject; multi-image; affine (Mutual Information) + multi-image B-spline transformation (Mutual Information and mean square difference); Giordano (2016)
par0045 MRI mouse brain inter and intra-subject, perfusion data; rigid + affine + B-spline transformation; Hirschler and Munting (2016)
par0046 3D QCT Human femur inter-subject, affine + B-spline transformation; Besler, et al. (2017)
par0047 4D DCE-MRI abdomen intra-subject; B-spline transformation; groupwise registration; PCA metric Jansen, et al. (submitted)
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