<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Registration</category>
  <title>ANTS Registration)</title>
  <description>ANTS (Advanced Normalization Tools) Registration</description>
  <version> 1.0</version>
  <documentation-url></documentation-url>
  <license>http://www.apache.org/licenses/LICENSE-2.0.txt</license>
  <contributor>Brian Avants, Jeff Duda, Gang Song, Sandhitsu Das, Jon Pluta, Nick Tustison, Hans Johnson, Kent Williams</contributor>
  <acknowledgements></acknowledgements>
 <parameters>
   <integer>
     <name>Dimensionality</name>
     <label>Dimensionality</label>
     <longflag>dimensionality</longflag>
     <description>This option forces the image to be treated as a
     specified-dimensional image.  If not specified, N4 tries to infer
     the dimensionality from the input image.</description>
     <default>3</default>
   </integer>
   <file>
     <name>OutputTransformPrefix</name>
     <longflag>outputTransformPrefix</longflag>
     <label>Output Transform Prefix</label>
     <channel>input</channel>
     <description>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.</description>
     <default></default>
   </file>
   <file multiple="true" >
     <name>InitialTransform</name>
     <longflag>initial-transform</longflag>
     <label>Initial Transforms</label>
     <channel>input</channel>
     <description>Specify the initial 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.  See
     antsApplyTransforms.  + std::string( "for additional
     information.</description>
     <default></default>
   </file>
   <string-enumeration multiple="true" >
    <name>ImageMetric</name>
    <label>Image Metrics</label>
    <longflag>metric</longflag>
    <description>These image metrics are available--- CC: ANTS
    neighborhood cross correlation, MI: Mutual information, and
    Demons: Thirion's Demons (modified mean-squares). GC, Global
    Correlation. Note that the metricWeight is currently not used.
    Rather, it is a temporary place holder until multivariate metrics
    are available for a single stage. The metrics can also employ a
    sampling strategy defined by a sampling percentage. The sampling
    strategy defaults to dense, 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. </description>
    <element>CC</element>
    <element>MI</element>
    <element>Mattes</element>
    <element>Demons</element>
    <element>GC</element>
    <default></default>
  </string-enumeration>
   <string-enumeration multiple="true" >
    <name>Transform</name>
    <label>Transform</label>
    <longflag>transform</longflag>
    <description>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.</description>
    <element>Rigid</element>
    <element>Affine</element>
    <element>CompositeAffine</element>
    <element>Similarity</element>
    <element>Translation</element>
    <element>GaussianDisplacementField</element>
    <element>BSplineDisplacementField</element>
    <element>TimeVaryingVelocityField</element>
    <element>Syn</element>
    <default></default>
  </string-enumeration>
  <float-vector>
    <name>SmoothingSigmas</name>
    <description>Specify the amount of smoothing at each level.</description>
    <longflag>smoothingSigmas</longflag>
    <default></default>
  </float-vector>
  <integer-vector>
    <name>ShrinkFactors</name>
    <description>Specify the shrink factor for the virtual domain
    (typically the fixed image) at each level.</description>
    <longflag>shrinkFactors</longflag>
    <default></default>
  </integer-vector>
  <boolean>
    <name>UseHistogramMatch</name>
    <longflag>useHistogramMatch</longflag>
    <description>Histogram match the images before registration.</description>
    <default>false</default>
  </boolean>
  <float-vector>
    <name>WinsorizeImageIntensities</name>
    <longflag>winsorizeImageIntensities</longflag>
    <description>Winsorize data based on specified quantiles.</description>
    <default></default>
  </float-vector>

</parameters>
</executable>
