<?xml version="1.0" encoding="utf-8" ?>
  <executable>
  <category>Registration</category>
  <title>BRAINSResample</title>

  <description>
This program resamples an image image using a deformation field or a linear transform.
  </description>
  <version>0.1</version>
  <documentation-url>http://www.nitrc.org/projects/brainsdemonwarp/</documentation-url>
  <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt </license>
  <contributor>This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson.</contributor>

  <parameters>
    <label>Input Image Files</label>
    <description>Parameters for specifying the deformation field, image to warp and resulting image space</description>

    <image>
      <name>inputVolume</name>
      <longflag>--inputVolume</longflag>
      <description>Image To Warp</description>
      <label>Image To Warp</label>
      <channel>input</channel>
    </image>

    <image>
      <name>referenceVolume</name>
      <longflag>--referenceVolume</longflag>
      <description>Reference image defining the output space</description>
      <label>Reference Image</label>
      <channel>input</channel>
    </image>

    <image>
      <name>deformationVolume</name>
      <longflag>--deformationVolume</longflag>
      <description>Deformation Field</description>
      <label>Deformation Field</label>
      <channel>input</channel>
      <default></default>
    </image>

  </parameters>

  <parameters>
    <label>Warping Parameters</label>
    <description>Parameters used to define home the image is warped</description>

    <file>
      <name>warpTransform</name>
      <longflag>--warpTransform</longflag>
      <label>Warp By Transform</label>
      <description>Filename for the BRAINSFit transform used in place of the deformation field</description>
      <channel>input</channel>
      <default></default>
    </file>

    <string-enumeration>
      <name>pixelType</name>
      <longflag>--pixelType</longflag>
      <label>Pixel Type</label>
      <description>Specifies the pixel type for the input/output images.  The "binary" pixel type uses a modified algorithm whereby the image is read in as unsigned char, a signed distance map is created, signed distance map is resampled, and then a thresholded image of type unsigned char is written to disk.</description>
      <default>uchar</default>
      <element>uchar</element>
      <element>short</element>
      <element>ushort</element>
      <element>int</element>
      <element>uint</element>
      <element>float</element>
      <element>binary</element>
    </string-enumeration>

    <string-enumeration>
      <name>interpolationMode</name>
      <longflag>interpolationMode</longflag>
      <label>Interpolation Mode</label>
      <description>Type of interpolation used</description>
      <default>Linear</default>
      <element>NearestNeighbor</element>
      <element>Linear</element>
      <element>BSpline</element>
      <element>WindowedSinc</element>
    </string-enumeration>

    <boolean>
      <name>invertTransform</name>
      <longflag>--invertTransform</longflag>
      <label>Invert Linear Transform flag</label>
      <description>Perform transform inversion in itk physical space before applying the linear transform to the image.</description>
      <default>false</default>
    </boolean>

    <float>
      <name>defaultValue</name>
      <longflag>defaultValue</longflag>
      <label>Default Value</label>
      <description>Default voxel value</description>
      <default>0.0</default>
    </float>
  </parameters>


  <parameters advanced="true">
    <label>Invalid Parameters</label>
    <description>These parameters just give an innocuous warning.</description>

    <string>
      <name>useTransformMode</name>
      <longflag>useTransformMode</longflag>
      <label>Explicit Transform Kind in Use</label>
      <description>This defunct parameter is no longer in service.  Now ApplyWarp infers the transform type from the contents of the .mat file.</description>
      <default></default>
    </string>

  </parameters>


  <parameters>
    <label>Result File</label>
    <description>Resulting deformed image</description>

    <file>
      <name>outputVolume</name>
      <longflag>--outputVolume</longflag>
      <description>Resulting deformed image</description>
      <label>Output Image</label>
      <channel>output</channel>
    </file>
  </parameters>

</executable>
