IGR3D_MABMIS_Testing.xml

<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Segmentation</category>
  <title>
    Multi-Atlas Based Group Segmentation -- Testing
  </title>
  <description>
    Refer to: "Iterative multi-atlas-based multi-image segmentation with tree-based registration", NeuroImage, 59(1):422–430, 2012.
  </description>
  <version></version>
  <documentation-url></documentation-url>
  <license></license>
  <contributor>Minjeong Kim, Dinggang Shen, Xiaofeng Liu</contributor>
  <acknowledgements>
    This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. This work is also supported by Grant R01 EB006733 from the National Institute of Biomedical Imaging and Bioengineering , National Institutes of Health, through the University of North Carolina, Chapel Hill.
  </acknowledgements>

  <parameters>
    <label> Registration Parameters </label>
    <description>Parameters used for registration</description>

    <integer-vector>
      <name>iterations</name>
      <flag>i</flag>
      <longflag>iterations</longflag>
      <description>Comma separated list of iterations, for low resolution, middle resolution, and high resolution. </description>
      <label>Iterations</label>
      <default>5,3,2</default>
    </integer-vector>

    <double>
      <name>SmoothingKernelSize</name>
      <flag>s</flag>
      <longflag>sigma</longflag>
      <description>The standard deviation for smoothing deformation field</description>
      <label>Smoothing Kernel Size</label>
      <default>1.5</default>
    </double>
  </parameters>

  <parameters>
    <label>Parameters for group segmentation</label>
    <description>Parameters for group segmentation</description>

    <file fileExtensions=".xml">
     <name>AtlaseTreeXML</name>
     <description>xml file of the multi-atlases after training </description>
     <label>Tree-structured Atlases</label>
     <channel>input</channel>
     <longflag>atlasTreeXML</longflag>
     <default></default>
   </file>

    <file fileExtensions=".xml">
      <name>ImageListXML</name>
      <description>xml file that contains a list of images to be segmented </description>
      <label>Image List</label>
      <channel>input</channel>
      <longflag>imageListXML</longflag>
      <default></default>
    </file>
  </parameters>

  <parameters>
    <label> Output </label>
    <description>Parameters for output</description>
    <directory>
      <name>OutputFolder</name>
      <flag>o</flag>
      <longflag>outputfolder</longflag>
      <description>Output path to save the segmenetation results</description>
      <label>Path to save segmentation results</label>
      <default></default>
    </directory>
  </parameters>

</executable>