--version
- Get Version Information.
-d, --dimensionality 2/3/4
- This option forces the image to be treated as a specified-dimensional
image. If not specified, we try to infer the dimensionality from the input
image.
-o, --output outputTransformPrefix
- [outputTransformPrefix,<outputWarpedImage>,<outputInverseWarpedImage>]
- Specify the output transform prefix (output format is .nii.gz ).
Optionally, one can choose to warp the moving image to the fixed space
and, if the inverse transform exists, one can also output the warped fixed
image. Note that only the images specified in the first metric call are
warped. Use antsApplyTransforms to warp other images using the resultant
transform(s). When a composite transform is not specified, linear
transforms are specified with a '.mat' suffix and displacement fields with
a 'Warp.nii.gz' suffix (and 'InverseWarp.nii.gz', when applicable. In
addition, for velocity-based transforms, the full velocity field is
written to file ('VelocityField.nii.gz') as long as the collapse
transforms flag is turned off ('-z 0').
-j, --save-state saveStateAsTransform
- Specify the output file for the current state of the registration. The
state file is written to an hdf5 composite file. It is specially useful if
we want to save the current state of a SyN registration to the disk, so we
can load and restore that later to continue the next registration process
directly started from the last saved state. The output file of this flag
is the same as the write-composite-transform, unless the last transform is
a SyN transform. In that case, the inverse displacement field of the SyN
transform is also added to the output composite transform. Again notice
that this file cannot be treated as a transform, and restore-state option
must be used to load the written file by this flag.
-k, --restore-state restoreStateAsATransform
- Specify the initial state of the registration which get immediately used
to directly initialize the registration process. The flag is mutually
exclusive with other initialization flags.If this flag is used, none of
the initial-moving-transform and initial-fixed-transform cannot be
used.
-a, --write-composite-transform 1/(0)
- Boolean specifying whether or not the composite transform (and its
inverse, if it exists) should be written to an hdf5 composite file. This
is false by default so that only the transform for each stage is written
to file. <VALUES>: 0
-p, --print-similarity-measure-interval
<unsignedIntegerValue>
- Prints out the CC similarity metric measure between the full-size input
fixed and the transformed moving images at each iteration a value of 0
(the default) indicates that the full scale computation should not take
placeany value greater than 0 represents the interval of full scale metric
computation. <VALUES>: 0
--write-interval-volumes
<unsignedIntegerValue>
- Writes out the output volume at each iteration. It helps to present the
registration process as a short movie a value of 0 (the default) indicates
that this option should not take placeany value greater than 0 represents
the interval between the iterations which outputs are written to the disk.
<VALUES>: 0
-z, --collapse-output-transforms (1)/0
- Collapse output transforms. Specifically, enabling this option combines
all adjacent transforms wherepossible. All adjacent linear transforms are
written to disk in the forman itk affine transform (called
xxxGenericAffine.mat). Similarly, all adjacent displacement field
transforms are combined when written to disk (e.g. xxxWarp.nii.gz and
xxxInverseWarp.nii.gz (if available)).Also, an output composite transform
including the collapsed transforms is written to the disk (called
outputCollapsed(Inverse)Composite). <VALUES>: 1
-i, --initialize-transforms-per-stage (1)/0
- Initialize linear transforms from the previous stage. By enabling this
option, the current linear stage transform is directly initialized from
the previous stage's linear transform; this allows multiple linear stages
to be run where each stage directly updates the estimated linear transform
from the previous stage. (e.g. Translation -> Rigid -> Affine).
<VALUES>: 0
- -n, --interpolation
Linear
- NearestNeighbor MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
Gaussian[<sigma=imageSpacing>,<alpha=1.0>]
BSpline[<order=3>] CosineWindowedSinc WelchWindowedSinc
HammingWindowedSinc LanczosWindowedSinc
GenericLabel[<interpolator=Linear>]
- Several interpolation options are available in ITK. These have all been
made available. Currently the interpolator choice is only used to warp
(and possibly inverse warp) the final output image(s).
-g, --restrict-deformation PxQxR
- This option allows the user to restrict the optimization of the
displacement field, translation, rigid or affine transform on a
per-component basis. For example, if one wants to limit the deformation or
rotation of 3-D volume to the first two dimensions, this is possible by
specifying a weight vector of '1x1x0' for a deformation field or
'1x1x0x1x1x0' for a rigid transformation. Low-dimensional restriction only
works if there are no preceding transformations.All stages up to and
including the desired stage must have this option specified,even if they
should not be restricted (in which case specify 1x1x1...)
- -q,
--initial-fixed-transform initialTransform
- [initialTransform,<useInverse>]
[fixedImage,movingImage,initializationFeature]
- Specify the initial fixed transform(s) which get immediately incorporated
into the composite transform. The order of the transforms is stack-esque
in that the last transform specified on the command line is the first to
be applied. In addition to initialization with ITK transforms, the user
can perform an initial translation alignment by specifying the fixed and
moving images and selecting an initialization feature. These features
include using the geometric center of the images (=0), the image
intensities (=1), or the origin of the images (=2).
- -r,
--initial-moving-transform initialTransform
- [initialTransform,<useInverse>]
[fixedImage,movingImage,initializationFeature]
- Specify the initial moving transform(s) which get immediately incorporated
into the composite transform. The order of the transforms is stack-esque
in that the last transform specified on the command line is the first to
be applied. In addition to initialization with ITK transforms, the user
can perform an initial translation alignment by specifying the fixed and
moving images and selecting an initialization feature. These features
include using the geometric center of the images (=0), the image
intensities (=1), or the origin of the images (=2).
-m, --metric
CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
- MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
Mattes[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
MeanSquares[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
Demons[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
GC[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]
ICP[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>]
PSE[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>,<pointSetSigma=1>,<kNeighborhood=50>]
JHCT[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>,<pointSetSigma=1>,<kNeighborhood=50>,<alpha=1.1>,<useAnisotropicCovariances=1>]
IGDM[fixedImage,movingImage,metricWeight,fixedMask,movingMask,<neighborhoodRadius=0x0>,<intensitySigma=0>,<distanceSigma=0>,<kNeighborhood=1>,<gradientSigma=1>]
- These image metrics are available--- CC: ANTS neighborhood cross
correlation, MI: Mutual information, Demons: (Thirion), MeanSquares, and
GC: Global Correlation. The "metricWeight" variable is used to
modulate the per stage weighting of the metrics. The metrics can also
employ a sampling strategy defined by a sampling percentage. The sampling
strategy defaults to 'None' (aka a dense sampling of one sample per
voxel), otherwise it defines a point set over which to optimize the
metric. The point set can be on a regular lattice or a random lattice of
points slightly perturbed to minimize aliasing artifacts.
samplingPercentage defines the fraction of points to select from the
domain. useGradientFilter specifies whether a smoothingfilter is applied
when estimating the metric gradient.In addition, three point set metrics
are available: Euclidean (ICP), Point-set expectation (PSE), and
Jensen-Havrda-Charvet-Tsallis (JHCT).
- -t, --transform
Rigid[gradientStep]
- Affine[gradientStep] CompositeAffine[gradientStep]
Similarity[gradientStep] Translation[gradientStep]
BSpline[gradientStep,meshSizeAtBaseLevel]
GaussianDisplacementField[gradientStep,updateFieldVarianceInVoxelSpace,totalFieldVarianceInVoxelSpace]
BSplineDisplacementField[gradientStep,updateFieldMeshSizeAtBaseLevel,<totalFieldMeshSizeAtBaseLevel=0>,<splineOrder=3>]
TimeVaryingVelocityField[gradientStep,numberOfTimeIndices,updateFieldVarianceInVoxelSpace,updateFieldTimeVariance,totalFieldVarianceInVoxelSpace,totalFieldTimeVariance]
TimeVaryingBSplineVelocityField[gradientStep,velocityFieldMeshSize,<numberOfTimePointSamples=4>,<splineOrder=3>]
SyN[gradientStep,<updateFieldVarianceInVoxelSpace=3>,<totalFieldVarianceInVoxelSpace=0>]
BSplineSyN[gradientStep,updateFieldMeshSizeAtBaseLevel,<totalFieldMeshSizeAtBaseLevel=0>,<splineOrder=3>]
Exponential[gradientStep,updateFieldVarianceInVoxelSpace,velocityFieldVarianceInVoxelSpace,<numberOfIntegrationSteps>]
BSplineExponential[gradientStep,updateFieldMeshSizeAtBaseLevel,<velocityFieldMeshSizeAtBaseLevel=0>,<numberOfIntegrationSteps>,<splineOrder=3>]
- Several transform options are available. The gradientStep or learningRate
characterizes the gradient descent optimization and is scaled
appropriately for each transform using the shift scales estimator.
Subsequent parameters are transform-specific and can be determined from
the usage. For the B-spline transforms one can also specify the smoothing
in terms of spline distance (i.e. knot spacing).
- -c, --convergence
MxNxO
- [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]
- Convergence is determined from the number of iterations per level and is
determined by fitting a line to the normalized energy profile of the last
N iterations (where N is specified by the window size) and determining the
slope which is then compared with the convergence threshold.
-s, --smoothing-sigmas MxNxO...
- Specify the sigma of gaussian smoothing at each level. Units are given in
terms of voxels ('vox') or physical spacing ('mm'). Example usage is
'4x2x1mm' and '4x2x1vox' where no units implies voxel spacing.
-f, --shrink-factors MxNxO...
- Specify the shrink factor for the virtual domain (typically the fixed
image) at each level.
-u, --use-histogram-matching
- Histogram match the images before registration.
-w, --winsorize-image-intensities
[lowerQuantile,upperQuantile]
- Winsorize data based on specified quantiles.
-x, --masks [fixedImageMask,movingImageMask]
- Image masks to limit voxels considered by the metric. Two options are
allowed for mask specification: 1) Either the user specifies a single mask
to be used for all stages or 2) the user specifies a mask for each stage.
With the latter one can select to which stages masks are applied by
supplying valid file names. If the file does not exist, a mask will not be
used for that stage. Note that we handle the fixed and moving masks
separately to enforce this constraint.
--float
- Use 'float' instead of 'double' for computations.
--minc
- Use MINC file formats for transformations. <VALUES>: 0
--random-seed seedValue
- Use a fixed seed for random number generation. By default, the system
clock is used to initialize the seeding. The fixed seed can be any nonzero
int value.
-v, --verbose (0)/1
- Verbose output.
-h
- Print the help menu (short version).
--help
- Print the help menu. Will also print values used on the current command
line call. <VALUES>: 1