COMMAND:¶

antsAI

Program to calculate the optimallinear transform parameters for aligning two images.

OPTIONS:¶

-d, --dimensionality 2/3

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.

-m, --metric MI[fixedImage,movingImage,<numberOfBins=32>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]

Mattes[fixedImage,movingImage,<numberOfBins=32>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>] GC[fixedImage,movingImage,<radius=NA>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]

These image metrics are available: MI: joint histogram and Mattes: mutual information and GC: global correlation.

-t, --transform Rigid[gradientStep]

Affine[gradientStep] Similarity[gradientStep] AlignGeometricCenters AlignCentersOfMass

Several transform options are available. For the rigid, affine, and similarity transforms, the gradientStep characterizes the gradient descent optimization and is scaled appropriately for each transform using the shift scales estimator. The other two transform types finds the simple translation transform which aligns the specified image feature. Note that the images are read from the similarity metric option although the metric isn't actually used.

-p, --align-principal-axes

Boolean indicating alignment by principal axes. Alternatively, one can align using blobs (see -b option).

-b, --align-blobs numberOfBlobsToExtract

[numberOfBlobsToExtract,<numberOfBlobsToMatch=numberOfBlobsToExtract>]

Boolean indicating alignment by a set of blobs. Alternatively, one can align using blobs (see -p option).

-s, --search-factor searchFactor

[searchFactor=20,<arcFraction=1.0>]

Incremental search factor (in degrees) which will sample the arc fraction around the principal axis or default axis.

-g, --translation-search-grid [stepSize=25, AxBxC=0x0x0]

Translation search grid in mm, which will translate the moving image in each dimension in increments of the step size.

-c, --convergence numberOfIterations

[numberOfIterations,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]

Number of iterations.

-x, --masks fixedImageMask

[fixedImageMask,movingImageMask]

Image masks to limit voxels considered by the metric.

-o, --output outputFileName

Specify the output transform (output format an ITK .mat file).

--random-seed seedValue

Use a fixed seed for random number generation. The default fixed seed is overwritten by this value. The fixed seed can be any nonzero int value. If the specified seed is zero, the system time will be used.

-v, --verbose (0)/1

Verbose output.

-h

Print the help menu (short version).

--help

Print the help menu. <VALUES>: 1