.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.5.
.TH ANTSAI "1" "October 2017" "antsAI 2.2.0" "User Commands"
.SH NAME
antsAI \- part of ANTS registration suite
.SH DESCRIPTION
.SS "COMMAND:"
.IP
antsAI
.IP
Program to calculate the optimallinear transform parameters for aligning two
images.
.SS "OPTIONS:"
.HP
\fB\-d\fR, \fB\-\-dimensionality\fR 2/3
.IP
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.
.HP
\fB\-m\fR, \fB\-\-metric\fR MI[fixedImage,movingImage,<numberOfBins=32>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
.IP
Mattes[fixedImage,movingImage,<numberOfBins=32>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
GC[fixedImage,movingImage,<radius=NA>,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
.IP
These image metrics are available: MI: joint histogram and Mattes: mutual
information and GC: global correlation.
.TP
\fB\-t\fR, \fB\-\-transform\fR Rigid[gradientStep]
Affine[gradientStep]
Similarity[gradientStep]
.IP
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.
.HP
\fB\-p\fR, \fB\-\-align\-principal\-axes\fR
.IP
Boolean indicating alignment by principal axes. Alternatively, one can align
using blobs (see \fB\-b\fR option).
.TP
\fB\-b\fR, \fB\-\-align\-blobs\fR numberOfBlobsToExtract
[numberOfBlobsToExtract,<numberOfBlobsToMatch=numberOfBlobsToExtract>]
.IP
Boolean indicating alignment by a set of blobs. Alternatively, one can align
using blobs (see \fB\-p\fR option).
.TP
\fB\-s\fR, \fB\-\-search\-factor\fR searchFactor
[searchFactor,<arcFraction=1.0>]
.IP
Incremental search factor (in degrees) which will sample the arc fraction around
the principal axis or default axis.
.TP
\fB\-c\fR, \fB\-\-convergence\fR numberOfIterations
[numberOfIterations,<convergenceThreshold=1e\-6>,<convergenceWindowSize=10>]
.IP
Number of iterations.
.HP
\fB\-x\fR, \fB\-\-masks\fR fixedImageMask
.IP
[fixedImageMask,movingImageMask]
.IP
Image masks to limit voxels considered by the metric.
.HP
\fB\-o\fR, \fB\-\-output\fR outputFileName
.IP
Specify the output transform (output format an ITK .mat file).
.HP
\fB\-v\fR, \fB\-\-verbose\fR (0)/1
.IP
Verbose output.
.HP
\fB\-h\fR
.IP
Print the help menu (short version).
.HP
\fB\-\-help\fR
.IP
Print the help menu.
<VALUES>: 1