<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Diffusion.Filtering</category>
  <title>Rician LMMSE Image Filter</title>
  <description>
    Filters a set of diffusion weighted images in the mean squared error sense using a Rician noise model. The noise parameter is automatically estimated. New version using ITK pipelines and multi-threading.
</description>
  <version>0.1.1.$Revision: 1 $(alpha)</version>
  <documentation-url></documentation-url>
  <license></license>
  <contributor>Antonio Tristan Vega, Santiago Aja Fernandez and Marc Niethammer. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia (Spain).</contributor>

  <parameters>
    <label>DWI Noise Removal Parameters</label>
    <description>Parameters for Rician LMMSE image filter</description>

    <integer>
      <name>iIterations</name>
      <label>Number of iterations</label>
      <longflag>--iter</longflag>
      <description>Number of iterations for the noise removal filter.</description>
      <default>1</default>
      <constraints>
  <minimum>0</minimum>
  <maximum>25</maximum>
  <step>1</step>
      </constraints>
    </integer>

    <integer-vector>
      <name>iRadiusEstimation</name>
      <label>Estimation Radius</label>
      <longflag>--re</longflag>
      <description>Estimation radius.</description>
      <default>3,3,0</default>
    </integer-vector>

    <integer-vector>
      <name>iRadiusFiltering</name>
      <label>Filtering Radius</label>
      <longflag>--rf</longflag>
      <description>Filtering radius.</description>
      <default>3,3,0</default>
    </integer-vector>

    <integer>
      <name>iMinimumNumberOfUsedVoxelsF</name>
      <label>Minimum voxels # for filtering.</label>
      <longflag>--mnvf</longflag>
      <description>Minimum number of voxels in kernel used for filtering.</description>
      <default>1</default>
    </integer>

    <integer>
      <name>iMinimumNumberOfUsedVoxelsE</name>
      <label>Minimum voxels # for estimation.</label>
      <longflag>--mnve</longflag>
      <description>Minimum number of voxels in kernel used for estimation.</description>
      <default>1</default>
    </integer>

    <integer>
      <name>dMinSTD</name>
      <label>Minimum noise STD.</label>
      <longflag>--minnstd</longflag>
      <description>Minimum allowed noise standard deviation.</description>
      <default>0</default>
    </integer>

    <integer>
      <name>dMaxSTD</name>
      <label>Maximum noise STD.</label>
      <longflag>--maxnstd</longflag>
      <description>Maximum allowed noise standard deviation.</description>
      <default>10000</default>
    </integer>

    <double>
      <name>dResFact</name>
      <label>Histogram resolution factor.</label>
      <longflag>--hrf</longflag>
      <description>How many histogram bins per unit interval.</description>
      <default>2.0</default>
    </double>

    <boolean>
      <name>bUseAbsoluteValue</name>
      <label>Use absolute value.</label>
      <longflag>--uav</longflag>
      <description>Use absolute value in case of negative square.</description>
      <default>true</default>
    </boolean>


  </parameters>

  <parameters>
    <label>IO</label>
    <description>Input/output parameters</description>
    <image type="diffusion-weighted">
      <name>inputVolume</name>
      <label>Input Volume</label>
      <channel>input</channel>
      <index>0</index>
      <description>Input DWI volume.</description>
    </image>
    <image type="diffusion-weighted">
      <name>outputVolume</name>
      <label>Output Volume</label>
      <channel>output</channel>
      <index>1</index>
      <description>Output DWI volume.</description>
    </image>

  </parameters>

</executable>
