ToolBoxes

This page lists the tools that are embedded in SuperElastix or are considered to be.

Embedded Toolboxes.
Name Full Name Url
elastix   http://elastix.isi.uu.nl/
NiftyReg   https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
ANTS (itkv4) Advanced Normalization Tools https://github.com/ANTsX/ANTs
SYN: Symmetric Normalization https://www.ncbi.nlm.nih.gov/pubmed/17659998
DMFFD: itkBSplineSyN https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870320/
DMFFD: itkTimeVaryingBSplineVelocityField  
itkTimeVaryingVelocityField  
Considered Toolboxes.
Name Full Name Url
MIRTK The Medical Image Registration ToolKit https://github.com/BioMedIA/MIRTK
plastimatch   http://plastimatch.org/
Variational ITK Variational Registration Framework http://www.insight-journal.org/browse/publication/917
Demons (itk)   https://itk.org/Doxygen/html/classitk_1_1DemonsRegistrationFilter.html
DiffeomorphicDemons http://www.insight-journal.org/browse/publication/154
PDEDeformableRegistration https://itk.org/Doxygen/html/classitk_1_1PDEDeformableRegistrationFilter.html
Symmetric Log-Domain Diffeomorphic Demons https://hal.inria.fr/hal-00813744/document
DRAMMS Deformable Registration via Attribute Matching and Mutual-Saliency Weighting http://www.med.upenn.edu/sbia/dramms.html
MIRORR Multimodal Image Registration using blOck-matching and Robust Regression http://aehrc.github.io/Mirorr/
Incompatible/Unclassified Toolboxes.
Name Full Name Url
ABSORB ABSORB for groupwise registration  
DROP Deformable Image Registration using Discrete Optimization  
DTI-DROID Deformable Registration using Orientation and Intensity Descriptors  
MIND Modality Independent Shape Descriptor for Multi-modal Deformable Registration http://www.ibme.ox.ac.uk/research/biomedia/julia-schnabel/Software
DEEDS Dense Displacement Sampling for Deformable Registration http://www.ibme.ox.ac.uk/research/biomedia/julia-schnabel/Software
uTIlzReg Diffeomorphic registration of 2D/3D nifti images http://www.ibme.ox.ac.uk/research/biomedia/julia-schnabel/Software
FLIRT FMRIB’s Linear Image Registration Tool  
FNIRT FSL non-linear registration tool  
FAIR flexible algorithms for image registration  
LDDMM The Large Deformation Diffeomorphic Metric Mapping tool  
DARTEL Diffeomorphic Anatomical Registration using Exponenial Lie algebra  
GS Geodesic shooting  
IRTK Image Registration Toolkit  
AIR Automatic Image Registration  
ART The Automatic Registration Toolbox  
SAFIR-FLIRT Fast and flexible image registration toolbox  
MIRT Medical Image Registration Toolbox for Matlab  
MIPAV Medical Image Processing, Analysis, and Visualization  
HAMMER Hierarchical Attribute Matching Mechanism for Elastic Registration  
Animal    
CVS FreeSurfer combined volumetric and surface-based (CVS) registration  
SICLE small deformation inverse consistent linear elastic  
SLE    
JRD-fluid    
NAMIC sandbox