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elastix specifications


Unique identifier OMICS_17376
Name elastix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 4.8
Stability Stable
Source code URL https://codeload.github.com/tacorna/taco/tar.gz/v0.7.0
Maintained Yes




No version available



  • person_outline Stefan Klein

Publications for elastix

elastix citations


Motion compensated micro CT reconstruction for in situ analysis of dynamic processes

Sci Rep
PMCID: 5955979
PMID: 29769576
DOI: 10.1038/s41598-018-25916-5

[…] nsion basis is constructed out of a B-spline tensor products, which are now used to approximate three displacement components,The MVF is thus described by a parameter vector field w¯=[wx,wy,wz]. The ‘elastix’ toolbox, which is also exposed to Python through the SimpleElastix module, was used to optimise this parameter vector towards a maximalistion of the ‘Normalised Cross Correlation’ (NCC) metri […]


NiftyNet: a deep learning platform for medical imaging

Comput Methods Programs Biomed
PMCID: 5869052
PMID: 29544777
DOI: 10.1016/j.cmpb.2018.01.025

[…] edical imaging file formats (e.g. ACR-NEMA (1985), Analyze 7.5 (1986), DICOM (1992) MINC (1992), and NIfTI (2001)). Toolsets to solve common challenges such as registration (e.g. NiftyReg , ANTs and elastix ), segmentation (e.g. NiftySeg ), and biomechanical modeling (e.g. ) are available for use as part of image analysis pipelines. Pipelines for specific research applications such as FSL for fu […]


The Additional Contribution of White Matter Hyperintensity Location to Post stroke Cognitive Impairment: Insights From a Multiple Lesion Symptom Mapping Study

Front Neurosci
PMCID: 5938410
PMID: 29765301
DOI: 10.3389/fnins.2018.00290

[…] red to the 1-mm T1 MNI-152 (Montreal Neurological Institute) template (Fonov et al., ). The registration procedure was performed with a linear registration followed by a non-linear registration using elastix (Klein et al., ), and the resulting transformations were combined to transform the corresponding lesion maps of AIL and WMHs to the MNI-152 template. Rigorous quality checks of the registratio […]


Dosimetric feasibility of 4DCT ventilation imaging guided proton therapy for locally advanced non small cell lung cancer

PMCID: 5918906
PMID: 29695284
DOI: 10.1186/s13014-018-1018-x

[…] ng the location of each tagged grid between the exhalation and the inhalation images. The DVF generated from seven DIR algorithms were compared to the ground truth DVF included Velocity, MIM, Mirada, Elastix and 3 other in-house built algorithms from DIRART toolbox as Double Force Demons, Improved Lucas-Kanade, and Iterative Optical Flow. Among all algorithm, the Multi-pass B-spline based deformab […]


Comparison of six fit algorithms for the intra voxel incoherent motion model of diffusion weighted magnetic resonance imaging data of pancreatic cancer patients

PLoS One
PMCID: 5884505
PMID: 29617445
DOI: 10.1371/journal.pone.0194590

[…] fram Research, Champaign, U.S.A.).All DWI images were denoised using a Rician adaptive non-local means filter [], developed for spatially varying noise due to i.e. parallel imaging, and registered in Elastix [,] for details).We tested two Bayesian algorithms: IVIM-Bayesian-log [,] and IVIM-Bayesian-lin []. The IVIM-Bayesian-log was an implementation from the Bayesian approach described in detail […]


Does setup on rectal wall improve rectal cancer boost radiotherapy?

PMCID: 5883297
PMID: 29615067
DOI: 10.1186/s13014-018-1011-4

[…] egistered to each daily scan, mimicking the set-up on bony anatomy which is performed prior to each fraction of radiotherapy. These rigid registrations were done using the ‘Euler’ registration of the Elastix toolkit []. Registration accuracy was checked by visual inspection of bony alignment and errors were found to be limited to one voxel.Using the transformation matrix of the registration, delin […]


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elastix institution(s)
Division of Image Processing (LKEB), Department of Radiology, Leiden University Medical Center, Leiden, Netherlands; Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC, Rotterdam, Netherlands; Intelligent Systems Group, Faculty of EEMCS, Delft University of Technology, Delft, Netherlands; Department of Radiology, Erasmus MC, Rotterdam, Netherlands
elastix funding source(s)
This research was funded by the Netherlands Organization for Scientific Research (NWO), grants NWO VENI 639.021.919 and 639.021.124 and NWO NRG-2010.02, and by an Erasmus MC grant on “Advanced MR neuroimaging in presenile dementia.”

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