AtroposMin is a project mainly written in C++ and SHELL, based on the View license.
Release 1.9.x --- svn release 793++
Homepage: http://www.picsl.upenn.edu/ANTS/
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 (publication on the way).
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:
svn checkout https://advants.svn.sourceforge.net/svnroot/advants ANTS
cvs -d :pserver:[email protected]:/cvsroot/Insight co Insight
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