algorithms for image registration: advanced normalization tools (ants) brian avants, nick tustison,...
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Algorithms for Image Registration:Advanced Normalization Tools (ANTS)
Brian Avants, Nick Tustison, Gang Song, James C. Gee
Penn Image Computing and Science LaboratoryDepartments of Radiology, University of Pennsylvania,
Philadelphia, PA, USA
Advanced Normalization Tools (ANTs)
• An open-source toolkit for low and high-dimensional image registration.
• Simple command-line user interface reflects the variational optimization equation.
• Few parameters for most applications.• Well-evaluated & focus on usability.• Large range of functionality – similarity
metrics, landmarks, multiple optimization terms, multiple transformation models.
Affine Registration
• Stochastic gradient descent (Klein, Staring, Pluim) for speed per iteration.
• Multi-start global optimization option (MMBIA 2007) for challenging problems.
• Mutual information similarity• Landmarks & cost-masking enabled• Mapping decomposed into Rotation, Shearing,
Translation: easily generates GL group subspaces.
Synthetic Database
95.480.8813.43.621.2350.0970.0390.019prior1 50
95.291.3814.94.571.5540.0930.040.021prior 50
64.970.666.582.011.6120.1560.0940.025mstart 200
94.380001.6850.2020.0950.044grad 0
mNCrNCrMSErMIdtdKdSdRStrategy
Image Similarity Metric (%)Transform parameters metric
48 images warped from the template, 256x256x124, Affine warping + random Bspline nonrigid warping.
Deformation Models
• Elastic, e.g. Demons method.• Exponential Map Diff, e.g. Ashburner’s Dartel.• Time-Dependent Diff, e.g. LDDMM.• Bi-directional Diff (Exp, T-D or greedy impl.)• All are available as optional transformation
models. • Models may also be combined, in some cases.
Similarity Metrics
ANTS -DIFF –m SSD(I,J,w1) –m MI(I,J,w2) –m LM(I,J,w3)
Diff Regularization
May be easily combined turned on/off, applied to different images etc
ANTS -m MI[CT.nii,PET.nii,32] -Exp -n 3 -i 10x10x10 -o PETtoCT
PET warped to CT
Unregistered PET and CT
Jacobian of transformation PET overlayed on CT
Original Pet TransmissionOriginal CT
Diffeomorphic Mapping
Difffeomorphism
Elastic Under-Normalization
OS & Input/Output Issues
• ITK-compatible – builds using standard ITK, cmake, etc.
• NIFTI/SIFTI friendly, using ITK I/O.• How do we deal with orientation, etc?• Experience has shown header information
(particularly origin, orientation, affine matrix) is not always “right.”
• We thus allow its use as an option.
Conclusion & Future Work
• Parallelization and memory-efficient.• Xml format for organizing processing/results.• Alternative optimization – gradient descent now.• To Obtain: seek “Advanced Normalization Tools
(ANTs)” at sourceforge.net also at NITRC.• References:
– Evaluation of 14 non-rigid registration algorithms, A Klein, et al in preparation.– B Avants, et al. Symmetric diffeomorphic image registration, 2008.– Euler-Lagrange equations of computational anatomy, M. I. Miller, et al, 2003.
Affine Transform Space Parameterization
• Affine Registration: T(x) = Ax + t• A = R x S x K.
– Rotation R: a unit quaternion vector – Scaling S: 3 scaling factors in each axis– Shearing K: 3 coefficients in the upper triangle.
Real Image Database
prior 50 mstart 200 grad0
template test image their difference
registration
differencing
67 images of elderly and neurodegenerative human brains, T1 MRI 1.5 T, 1x1x1.5mm,
256x256x124.
93.441.1311.602.99prior1 50
93.671.2414.103.11prior 50
92.970.617.040.98mstart 200
92.29000grad 0
mNCrNCrMSErMIStrategy
Image Similarity Metric (%)