TissueClassification.xml

<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Segmentation</category>
  <title>Fuzzy Tissue Classification</title>
  <description>
    This module computes voxel by voxel tissue classification of an MR brain image using a fuzzy c-means algortihm. Bias field is modeled as a lower order polynomial. Bias field and tissue classification are estimated iteratively in an EM fashion. Internally, each voxel is assigned tissue membership function values, which range from 0 to 1. At any voxel, the sum of membership function of all classes is either 0 (outside of brain), or 1. The membership functions are converted in tissue labels to generate hard segmentation. 
</description>
  <version>3.0</version>
  <documentation-url>http://wiki.slicer.org/slicerWiki/index.php/Modules:FuzzySegmentationModule</documentation-url>
  <license>slicer3</license>
  <contributor>Xiaodong Tao, taox @ research . ge . com</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. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.
</acknowledgements>
<parameters>
  <label>IO</label>
  <description>Input/output parameters</description>
  <image>
    <name>inputVolume</name>
    <label>Input Volume</label>
    <channel>input</channel>
    <index>0</index>
    <description>Input T1 Image.</description>
  </image>

  <image type="label">
    <name>maskVolume</name>
    <label>Input mask</label>
    <channel>input</channel>
    <index>1</index>
    <description>Only voxels inside the mask are classified</description>
  </image>


  <image type="label">
    <name>brainLabel</name>
    <label>Hard Segmentation</label>
    <channel>output</channel>
    <index>2</index>
    <description>Output brain mask map.</description>
  </image>

  <image>
    <name>biasFieldFile</name>
    <label>Bias Field</label>
    <channel>output</channel>
    <index>3</index>
    <description>Estimated bias field</description>
  </image>
</parameters>

<parameters>
  <label>Tissue classification Parameters</label>
  <description>Parameters used for tissue classification.</description>
  <integer>
    <name>nClasses</name>
    <flag>-c</flag>
    <longflag>--class</longflag>
    <description>Number of classes</description>
    <label>NumberOfClasses</label>
    <default>3</default>
  </integer> 

  <integer>
    <name>nBiasOption</name>
    <flag>-b</flag>
    <longflag>--biasoption</longflag>
    <description>Option for bias correction (0: no bias correction; 1: global linear; 2: global quadratic; 3: region based linear; 4: region based quadratic)</description>
    <label>BiasOption</label>
    <default>0</default>
    <constraints>
      <minimum>0</minimum>
      <maximum>4</maximum>
    </constraints>
  </integer>

</parameters>
</executable>