<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Registration</category>
  <title>DTI Registration (SBIA, UPenn)</title>
  <description> A module to register DT images by geometry features. For details of the algorithm, please refer to J. Yang, D. Shen, C. Davatzikos, and R. Verma, "Diffusion tensor image registration using tensor geometry and orientation feature," MICCAI 2008.
</description>
  <version>1.0</version>
  <documentation-url></documentation-url>
  <license></license>
  <contributor>SBIA </contributor>
  <acknowledgements> SBIA </acknowledgements>
 <parameters>
    <label>Input/Output</label>
    <description>Input/output parameters</description>
    <image type="tensor">
      <name>DTIRegistrationInputModel</name>
      <label>Model Volume (template)</label>
      <channel>input</channel>
      <flag>-M</flag>
      <longflag>--model</longflag>
      <default>None</default>
      <description>Input Model DTI</description>
    </image>
    <image type="tensor">
      <name>DTIRegistrationInputSubject</name>
      <label>Subject Volume (subject)</label>
      <channel>input</channel>
      <flag>-S</flag>
      <longflag>--subject</longflag>
      <default>None</default>
      <description>Input Subject DTI</description>
    </image>
    <image type="tensor">
      <name>DTIRegistrationOutputRegistered</name>
      <label>Registered Volume</label>
      <channel>output</channel>
      <flag>-O</flag>
      <longflag>--registered</longflag>
      <default>None</default>
      <description>Output Registered DTI</description>
    </image>
</parameters>

<parameters advanced="true">
  <label>Parameters of the Registration</label>
  <description>Parameters of the Registration</description>
  <integer-vector>
      <name>iteration</name>
      <flag>-I</flag>
      <longflag>--iteration</longflag>
      <description>set the number of iterations of the registration</description>
      <label>iterations on geometry and rotation feature (Geo,Rot):</label>
      <default>50,0</default>
    </integer-vector>

     <float>
      <name>StepRatio</name>
      <flag>-R</flag>
      <longflag>--StepRation</longflag>
      <description> step ratio, default: 0.02</description>
      <label> step ratio:</label>
      <default>0.02</default>
    </float>

   <integer-vector>
      <name>neighborhood</name>
      <flag>-r</flag>
      <longflag>--neighbor</longflag>
      <description>neighborhood search size, different at each resolution</description>
      <label>neighborhood search size at each resolution (low,mid,high):</label>
      <default>12,10,8</default>
    </integer-vector>

   <float>
      <name>similarity</name>
      <flag>-m</flag>
      <longflag>--SimilarityDegree</longflag>
      <description> the similarity degree</description>
      <label> similarity degree:</label>
      <default>0.75</default>
    </float>

   <float>
      <name>smoothness</name>
      <flag>-c</flag>
      <longflag>--SmoothnessFactor</longflag>
      <description> smoothness factor of the deformation field</description>
      <label> smoothness factor of the deformation field ([0,1], 1 is the smoothest):</label>
      <default>0.5</default>
    </float>

   <integer>
      <name>smoothnessDeform</name>
      <flag>-E</flag>
      <longflag>--SmoothingTime</longflag>
      <description>  times for smoothing deformation fields</description>
      <label>  times for smoothing deformation fields:</label>
      <default>1</default>
    </integer>
</parameters>

</executable>
