See the new ants website
Experimental transition to github for development: Wed Jan 23 10:46:13 EST 2013
Release 1.9.x --- final svn release = 1781, now moved to git ....
Introduction -- ANTS is a tool for computational neuroanatomy based on medical images. ANTS reads any image type that can be read by ITK (www.itk.org), that is, jpg, tiff, hdr, nii, nii.gz, mha/d and more image types as well. For the most part, ANTS will output float images which you can convert to other types with the ANTS ConvertImagePixelType tool. ImageMath has a bunch of basic utilities such as multiplication, inversion and many more advanced tools such as computation of the Lipschitz norm of a deformation field. ANTS programs may be called from the command line on almost any platform .... you can compile the code yourself or use the precompiled binaries for Windows (Vista), OSX (Darwin) or linux (32 bit or 64 bit). Download the binaries that are correct for you. If you are a naive user (not from a medical imaging background) then you might still find the tools here useful. Many of the operations available, for instance, in PhotoShop are available in ANTS and many more are available as well. For instance, ANTS tools may be useful in face mapping / morphing and also in generating animations from two different images, for instance, interpolating between frames in a movie. But, mainly, ANTS is useful for brain mapping, segmentation, measuring cortical thickness and in generating automated or semi-automated labeling of three-dimensional imagery (e.g. labeling hippocampus or cortical regions or lobes of the lung). Many prior-based segmentation possibilities are available in the Atropos tool, including three tissue segmentation, structure-specific segmentation and brain extracton.
The ants.pdf file has more details and examples.
New Stuff 1.9.x : Requires git-itk. must be compiled with USE_REVIEW on.
official release of atropos segmentation tool.
checked compilation on windows os.
we now save vector nii.gz files and do not store component images.
improves ImageMath tensor functions.
many operations may be performed on vector images.
some enhancements include:
you can warp a vector field represented as a nii.gz via WarpImageMultiTransform
MeasureMinMaxMean and MultiplyImages support vector images.
the only functionality that we "lost" is the ability to use a bspline interpolator with WIMT. the BSplineInterpolateImageFunction doesnt support vector valued pixels.
Atropos updated and validated.
New Stuff 1.9.2 :
New atropos interface + ROIStatistics in ImageMath
New Stuff 1.9.1 :
Atropos refactored , vtk dependencies allowed , additional tools for surface-based mapping (not much tested), augmented warping for vtk files
Must compile ITK with USE_REVIEW_STATISTICS ON if you want Atropos functionality Should compile ITK with USE_REVIEW ON Should compile ITK with USE_OPTIMIZED_REGISTRATION ON Should have ITK v 3.20 or greater.
New Stuff 1.9 :
Atropos revisions + various utilities.
New Stuff 1.8 :
Sped up CC metric -- comparable to PR but faster.
Fixed the MI metric -- fast and functional.
WarpTimeSeries --- for deforming 4D or vector images.
New Stuff 1.7 :
Now using SymmetricSecondOrderPixelType -- fixes some DT bugs with Nifti I/O etc.
This means our nii tensors have SYMMATRIX as intent (as with standard)
Update in parameters for convergence and inversion -- aids performance.
TensorToVector coloring --- also preliminary integration of vector field
Speed up number one for the CC metric (number two coming later).
Atropos ! new tool for segmentation.
Nick's N4 bias correction tool.
Updates to buildtemplateparallel that allow parallel use on multicore machines.
Various utilities and a few improvements in usage.
New Stuff 1.6 :
Check DT tensor ordering in DTI Read/Write
HistogramMatching in ImageMath
ConvertImagePixelType utility
Affine averaging in buildtemplateparallel
Updated time-dependent diffeomorphic mapping (option --geodesic 1 / 2 ).
Updated with a greedy exponential mapping diffeomorphic approach akin to DiffeomorphicDemons.
Bug fix in checking ANTS convergence.
Other miscellaneous including minor Apocrita changes and allowing spaces in command line interface.
Documentation -- pdf / tex describing ANTS Examples -- the executable programs and test data in Examples/Data Scripts -- user-friendly scripts for template building and running studies Utilities --- basic utilities ImageRegistration -- base code for ImageRegistration Temporary -- where temporary code lives Tensor -- base code for diffusion tensor operations
Use cmake (cmake.org) to set up compilation. To build ANTS, do the following:
- get ANTS
svn checkout https://advants.svn.sourceforge.net/svnroot/advants ANTS
- get itk :
cvs -d :pserver:anoncvs@www.itk.org:/cvsroot/Insight co Insight
- compile itk and ANTS -- link ANTS to itk build directory
ccmake ANTS/Examples/
-
call ctest in the compile directory and verify that the tests pass
-
in general, to perform a mapping :
ANTS 3 -m PR[tp22_s1.nii,template.nii.gz,1,4] -i 50x20x10 -o tp22map -t SyN[0.25] -x mask.nii.gz -r Gauss[3,0]
WarpImageMultiTransform 3 tp22_s1.nii tp22totemplate.nii -R template.nii.gz -i tp22mapAffine.txt tp22mapInverseWarp.nii
WarpImageMultiTransform 3 template.nii.gz templatetotp22.nii -R tp22_s1.nii tp22mapWarp.nii tp22mapAffine.txt
References:
ANTs registration
Principal references http://www.ncbi.nlm.nih.gov/pubmed/20851191 Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage. 2011 Feb 1;54(3):2033-44. doi: 10.1016/j.neuroimage.2010.09.025.
http://link.springer.com/chapter/10.1007/978-3-642-31340-0_28
Brian B. Avants, Nicholas J. Tustison, Gang Song, Baohua Wu, Michael Stauffer,
Matthew McCormick, Hans J. Johnson, James C. Gee.
A Unified Image Registration Framework for ITK.
Proceedings of the Fifth Workshop on Biomedical Image Registration 2012:266-275.
Symmetric Normalization (SyN) http://www.ncbi.nlm.nih.gov/pubmed/17659998 Avants BB, Epstein CL, Grossman M, Gee JC. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal. 2008 Feb;12(1):26-41.
B-spline-based http://www.ncbi.nlm.nih.gov/pubmed/19171516 Tustison NJ, Avants BB, Gee JC. Directly manipulated free-form deformation image registration. IEEE Trans Image Process. 2009 Mar;18(3):624-35. doi: 10.1109/TIP.2008.2010072.
http://link.springer.com/chapter/10.1007%2F978-3-642-31340-0_4
Nicholas J. Tustison, Brian B. Avants:
Diffeomorphic Directly Manipulated Free-Form Deformation Image Registration
via Vector Field Flows.
Proceedings of the Fifth Workshop on Biomedical Image Registration 2012:31-39.
Point set registration Point-set expectation (PSE) http://www.ncbi.nlm.nih.gov/pubmed/19437413 Pluta J, Avants BB, Glynn S, Awate S, Gee JC, Detre JA. Appearance and incomplete label matching for diffeomorphic template based hippocampus segmentation. Hippocampus. 2009 Jun;19(6):565-71. doi: 10.1002/hipo.20619.
Havrda-Charvat-Tsallis (JTB)
http://www.ncbi.nlm.nih.gov/pubmed/20937578
Tustison NJ, Awate SP, Song G, Cook TS, Gee JC.
Point set registration using Havrda-Charvat-Tsallis entropy measures.
IEEE Trans Med Imaging. 2011 Feb;30(2):451-60. doi: 10.1109/TMI.2010.2086065.
Template construction http://www.ncbi.nlm.nih.gov/pubmed/15501083 Avants B, Gee JC. Geodesic estimation for large deformation anatomical shape averaging and interpolation. Neuroimage. 2004;23 Suppl 1:S139-50.
http://www.ncbi.nlm.nih.gov/pubmed/19818860 Avants BB, Yushkevich P, Pluta J, Minkoff D, Korczykowski M, Detre J, Gee JC. The optimal template effect in hippocampus studies of diseased populations. Neuroimage. 2010 Feb 1;49(3):2457-66. doi: 10.1016/j.neuroimage.2009.09.062.
http://www.ncbi.nlm.nih.gov/pubmed/18995188 Avants B, Duda JT, Kim J, Zhang H, Pluta J, Gee JC, Whyte J. Multivariate analysis of structural and diffusion imaging in traumatic brain injury. Acad Radiol. 2008 Nov;15(11):1360-75. doi: 10.1016/j.acra.2008.07.007.
Atropos (n-tissue multivariate segmentation) http://www.ncbi.nlm.nih.gov/pubmed/21373993 Avants BB, Tustison NJ, Wu J, Cook PA, Gee JC. An open source multivariate framework for n-tissue segmentation with evaluation on public data. Neuroinformatics. 2011 Dec;9(4):381-400. doi: 10.1007/s12021-011-9109-y.
N4 bias correction http://www.ncbi.nlm.nih.gov/pubmed/20378467 Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC. N4ITK: improved N3 bias correction. IEEE Trans Med Imaging. 2010 Jun;29(6):1310-20. doi: 10.1109/TMI.2010.2046908.
DiReCT aka KellyKapowski/KellySlater http://www.ncbi.nlm.nih.gov/pubmed/19150502 Das SR, Avants BB, Grossman M, Gee JC. Registration based cortical thickness measurement. Neuroimage. 2009 Apr 15;45(3):867-79. doi: 10.1016/j.neuroimage.2008.12.016.
SCCAN http://www.ncbi.nlm.nih.gov/pubmed/20083207 Avants BB, Cook PA, Ungar L, Gee JC, Grossman M. Dementia induces correlated reductions in white matter integrity and cortical thickness: a multivariate neuroimaging study with sparse canonical correlation analysis. Neuroimage. 2010 Apr 15;50(3):1004-16. doi: 10.1016/j.neuroimage.2010.01.041.
SurfaceCurvature http://www.ncbi.nlm.nih.gov/pubmed/15344450 Avants B, Gee J. The shape operator for differential analysis of images. Inf Process Med Imaging. 2003 Jul;18:101-13.
Topological well-composedness http://www.ncbi.nlm.nih.gov/pubmed/21118779 Tustison NJ, Avants BB, Siqueira M, Gee JC. Topological well-composedness and glamorous glue: a digital gluing algorithm for topologically constrained front propagation. IEEE Trans Image Process. 2011 Jun;20(6):1756-61. doi: 10.1109/TIP.2010.2095021.
ANTs-related Studies http://www.ncbi.nlm.nih.gov/pubmed/15948659 Avants BB, Schoenemann PT, Gee JC. Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex. Med Image Anal. 2006 Jun;10(3):397-412. Epub 2005 Jun 3.
http://www.ncbi.nlm.nih.gov/pubmed/19195496 Klein A, Andersson J, Ardekani BA, Ashburner J, Avants B, Chiang MC, Christensen GE, Collins DL, Gee J, Hellier P, Song JH, Jenkinson M, Lepage C, Rueckert D, Thompson P, Vercauteren T, Woods RP, Mann JJ, Parsey RV. Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. Neuroimage. 2009 Jul 1;46(3):786-802. doi: 10.1016/j.neuroimage.2008.12.037.
http://www.ncbi.nlm.nih.gov/pubmed/20123029 Klein A, Ghosh SS, Avants B, Yeo BT, Fischl B, Ardekani B, Gee JC, Mann JJ, Parsey RV. Evaluation of volume-based and surface-based brain image registration methods. Neuroimage. 2010 May 15;51(1):214-20. doi: 10.1016/j.neuroimage.2010.01.091.
http://www.ncbi.nlm.nih.gov/pubmed/23151955 Tustison NJ, Avants BB, Cook PA, Kim J, Whyte J, Gee JC, Stone JR. Logical circularity in voxel-based analysis: Normalization strategy may induce statistical bias. Hum Brain Mapp. 2012 Nov 14. doi: 10.1002/hbm.22211.
http://www.ncbi.nlm.nih.gov/pubmed/17999940 Kim J, Avants B, Patel S, Whyte J, Coslett BH, Pluta J, Detre JA, Gee JC. Structural consequences of diffuse traumatic brain injury: a large deformation tensor-based morphometry study. Neuroimage. 2008 Feb 1;39(3):1014-26. Epub 2007 Oct 13.
gource ./ -s 0.05 --stop-at-end --output-ppm-stream ants.ppm ffmpeg -y -f image2pipe -vcodec ppm -i ants.ppm -vcodec mpeg4 -preset slow -crf 2 -b:v 4M ./ants_gource.mp4