<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Quantification.Musculoskeletal</category>
  <index>0</index>
  <title>Cancellous Analysis</title>
  <description><![CDATA[Perform Musculoskeletal Cancellous Analysis on an image]]></description>
  <version>0.1.0.</version>
  <documentation-url>https://github.com/username/project</documentation-url>
  <license/>
  <contributor>Joseph Szatkowski (Washington University in St. Louis)</contributor>
  <acknowledgements>
    <![CDATA[Developed by the Washington University in St. Louis Musculoskeletal Reseach Center with the assistance of Michael Brodt, Anish Jagannathan, Matthew Silva, and Simon Tang.\n
        This file was partially funded by NIH grant P30 AR074992.]]></acknowledgements>
  <parameters>
    <image>
      <name>image</name>
      <label>Image</label>
      <channel>input</channel>
      <index>0</index>
      <description><![CDATA[The image to be analyzed]]></description>
      <default>1.0</default>
    </image>
    <image type="label" reference ="image">
      <name>mask</name>
      <label>Mask</label>
      <channel>input</channel>
      <index>1</index>
      <description><![CDATA[Mask representing only the bone (not the medullary cavity) with pores covered]]></description>
    </image>
    <float>
      <name>lowerThreshold</name>
      <label>Lower Threshold</label>
      <channel>input</channel>
      <index>2</index>
      <description><![CDATA[The lower threshold for bone in the image]]></description>
    </float>
    <float>
      <name>upperThreshold</name>
      <label>Upper Threshold</label>
      <channel>input</channel>
      <index>3</index>
      <description><![CDATA[The upper threshold for bone in the image]]></description>
    </float>
    <float>
      <name>voxelSize</name>
      <label>Voxel Size</label>
      <channel>input</channel>
      <index>4</index>
      <description><![CDATA[The length of 1 voxel side in mm]]></description>
    </float>
    <float>
      <name>slope</name>
      <label>Slope</label>
      <channel>input</channel>
      <index>5</index>
      <description><![CDATA[The slope for density conversion]]></description>
    </float>
    <float>
      <name>intercept</name>
      <label>Intercept</label>
      <channel>input</channel>
      <index>6</index>
      <description><![CDATA[The slope intercept for density conversion]]></description>
    </float>
    <string>
      <name>inputName</name>
      <label>Input Name</label>
      <channel>input</channel>
      <index>7</index>
      <description><![CDATA[The name of the input image]]></description>
    </string>
    <string>
      <name>output</name>
      <label>Output Directory</label>
      <channel>input</channel>
      <index>8</index>
      <description><![CDATA[The directory to output data files to]]></description>
    </string>
  </parameters>
</executable>