Advanced Normalization Tools (ANTs)

ANTs extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized multimodality image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute. A summary of some ANTs findings and tutorial material (most of which is on this page) is here.

~ Source: ANTs webpage

Installation

http://brianavants.wordpress.com/

Once you’ve compiled the binaries, you can copy the bin folder and the lib folder here: /usr/local/ants/.

In case you have previously installed ANTs binaries into /usr/bin and you would like to remove them without manually do each for each file, here is a python script that does it.

To copy ants binaries for SCT, go to your antsbin folder. Then, copy the build_ants_sct.sh script found in SCT_DIR/bin/osx or linux and then execute it.

Parameters for antsRegistration

transform

-transform SyN[gradientStep, updateFieldVarianceInVoxelSpace, totalFieldVarianceInVoxelSpace]

gradientStep: the higher, the more high frequency deformations (and less stable)

updateFieldVarianceInVoxelSpace (default=3) –> the higher, the less high frequency deformations.

totalFieldVarianceInVoxelSpace: default=0.

  Exponential[1,5,5]
  • does not seem to move a lot

  BSplineSyN[0.1,5,5,2]

gradientStep: 0.5 –> the smaller, the smaller the distortion

updateFieldMeshSizeAtBaseLevel:

totalFieldMeshSizeAtBaseLevel: The larger, the larger the deform.

splineOrder=3

metric

-metric CC[x, x, weight, radius]

weight: 1. This param has no influence if there is only one transform.

radius: 4

CC is much slower than MI on large images.

  MI[x,x,weight,nbBins]

nbBins: 32

  • fast! however, does not work if using small mask (not enough values).

smoothing-sigmas

-smoothing-sigmas

  • Can have a HUGE impact on the result. Don’t hesitate to try without smoothing, i.e., 0x0 (if you have 2 iterations).

convergence

-convergence 20×3 –shrink-factors 2×1 –smoothing-sigmas 1x1mm –Restrict-Deformation 1x1x0 –output [tmp_reg,tmp.src_pad_reg.nii] –collapse-output-transforms 1 –interpolation BSpline[3] –winsorize-image-intensities [0.005,0.995]

Visualizing Warping Field

ANTs saves the warping field as a component image (5D), not in vector format (4D). Therefore, it cannot be interpreted by FSL. To convert the warping field in component, you can use c3d:

c3d -mcs warp_comp.nii -oo warp_vecx.nii warp_vecy.nii warp_vecz.nii

To convert vector-based warping field into component image readable by ANTS, use the following command

c3d warp_vecx.nii warp_vecy.nii warp_vecz.nii -omc 3 warp_comp.nii

Translation

-t Translation[GradientStep]

Example:

antsRegistration -d $ImageDimension -r [${FILE_DEST}.${EXT},${FILE_SRC}.${EXT} ,1] -m ${MetricType}
${FILE_DEST}.${EXT},${FILE_SRC}.${EXT},1,4] -o $OutPrefix -t Translation -c [10000x10000x10000,1.e-8,20] -s 4x2x1vox -f 3x2x1

Restrict Gradient Deformation

–Restrict-Deformation XxYxZ

Example: restrict the gradient in two dimensions (axial)

ants $ImageDimension -m ${MetricType}[${FILE_DEST}.${EXT_ANAT},${FILE_SRC}.${EXT},1,4] --Restrict-Deformation 1x1x0 -t SyN -r Gauss[6,3] -o ${PATH_OUTPUT}/ -i ${MaxIteration}

Note: this restriction does not apply to the affine transformation

Point-Set Expectation (PSE)

From the ANTs Manual PDF:

-m PSE [fixedImage, movingImage, fixedPoints, movingPoints, weight, pointSetPercentage, pointSetSigma, boundaryPointsOnly, kNeighborhood, PartialMatchingIterations=100000]

fixedImage: defines the space domain of the fixed point set.

movingImage: defines the space domain of the moving point set.

fixedPoints/Image: defines the coordinates of the fixed point set or label image. It can be an image with discrete positive labels, a VTK format point set file, or a text file. Details can be found in I/O section (TODO).

movingPoints/Image: defines the coordinates of the moving point set or label image.

weight: weight for this metric. 1 weights are relative to the weights on the N other metrics passed to ANTs — N is unlimited.

pointSetPercentage: the percentage of points to be randomly sampled used in the registration.

pointSetSigma: the standard deviation of the Parzen window used to estimate the expectation.

boundaryPointsOnly: 1 (or “true”) means only the boundary points in the label image is used to drive registration.

kNeighborhood is a positive discrete number. The first k neighbours are used to compute the deformation during the registration.

PartialMatchingIterations controls the symmetry in the matching. This option assumes the complete labeling is in the first set of label parameters … more iterations leads to more symmetry in the matching - 0 iterations means full asymmetry

Example

ants 3 -m PSE[destination.nii,source.nii,mask_destination.nii,mask_source.nii,0.8,100,1,0,1,100000] -o source_reg -i 0 --rigid-affine true --number-of-affine-iterations 100x10x5 -m MI[destination.nii,source.nii,0.2,4] --use-all-metrics-for-convergence 1

This line does an affine registration of the moving to the fixed image. There are 2 metrics used: PSE (point-set expectation) and MI (mutual information). The weight of each of them is the first “non-string” argument (0.8 for PSE and 0.2 for MI here). To do a diffeomorphic transformation, change the -i paramater to something like 50x50x50 (number of iteration to do for the diffeomorphic transformation). The MARKER files can be done with the ITK-snap labelling utility

 # apply the transformation
 WarpImageMultiTransform $DIM ${FILE_SRC}.${EXT} ${FILE_SRC}_reg_diffeo.${EXT} -R ${FILE_DEST}.${EXT} --use-BSpline
 ${FILE_SRC}Warp.nii.gz ${FILE_SRC}Affine.txt

This line applies the affine transformation to the moving image. For a diffeomorphic case, simply add ${FILE_SRC}Warp.nii.gz in the transformation parameter (end of the line)

Affine-only point-match transformation

Cannot be done with ANTs. Use the following command:

ANTSUseLandmarkImagesToGetAffineTransform fixed_image moving_image affine regAffine.txt

Non-affine point-match transformation

Alternatively to ANTS, you can use the following command:

ANTSUseLandmarkImagesToGetBSplineDisplacementField

Note: Images should be in the same space! Otherwise you receive a Segmentation 11 error. Suggestion is to first run ANTSUseLandmarkImagesToGetAffineTransform, then this command.

ITK Transform File

The FixedCenterOfRotationAffineTransform performs the following computation:

X′ =(S·X −C)+C+V

Where R is the rotation matrix, S is a scaling factor, C is the center of rotation and V is a translation vector or offset. Therefore the affine matrix M and the affine offset T are defined as:

M=R·S
T =C+V−R·C

NOTES ON ITK Transform Files:

T2d = [
a b o
c d p
0 0 1
]

T3d = [
a b c o
d e f p
g h i q
0 0 0 1
]

The “o p q” are the “offset”, which actually is not given in the file. The offset is computed from the 3×3 matrix (the first 9 parameters), from the translation “l m n” (the last three parameters), and from the center “x y z” (the three fixed parameters). To see how this is done, look at the code for ComputeOffset() itkMatrixOffsetTransformBase.hxx.

How centered transforms work: p’ = R (p - C) + C + T where p’ = transformed point, p = original point, C = Center, T= Translation. R= Rotation matrix.

Format for 2d affine transfo:

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_2_2
Parameters: a b c d o p
FixedParameters: 0 0

Format for 3d affine transfo:

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: a b c d e f g h i o p q
FixedParameters: 0 0

Documentation:

  1. ITK Documentation (700 pages): https://itk.org/ItkSoftwareGuide.pdf

  2. https://itk.org/Wiki/ITK/ImageRegistration

  3. http://public.kitware.com/pipermail/insight-users/2014-January/049703.html

Conversion world-image coordinate:

  1. http://www.vtk.org/Wiki/Proposals:Orientation

Discussions about ITK world coordinates:

  1. https://sourceforge.net/p/advants/discussion/840261/thread/2a1e9307/

  2. https://sourceforge.net/p/advants/discussion/840261/thread/ee4a6455/