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SkullStripper.xml
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SkullStripper.xml
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<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>Segmentation</category>
<title>SkullStripper</title>
<description><![CDATA[Skull stripping for structural MR images of the brain, tested on T1 and T2 contrast.]]></description>
<version>0.1.0</version>
<documentation-url>http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SkullStripper</documentation-url>
<license>Slicer</license>
<contributor>Xiaodong Tao (GE)</contributor>
<acknowledgements><![CDATA[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.]]></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 MR Image.</description>
</image>
<geometry>
<name>brainSurface</name>
<label>Output brain surface</label>
<channel>output</channel>
<index>1</index>
<description>Brain surface</description>
</geometry>
<image type="label">
<name>brainMask</name>
<label>Brain Mask</label>
<channel>output</channel>
<index>2</index>
<description>Output brain mask map.</description>
</image>
</parameters>
<parameters>
<label>Skull Stripping Parameters</label>
<description>Parameters used for skull stripping.</description>
<integer>
<name>nIterations</name>
<label>Iterations</label>
<flag>-i</flag>
<longflag>--iteration</longflag>
<description>Number of deformation iterations</description>
<default>100</default>
<constraints>
<minimum>0</minimum>
</constraints>
</integer>
<integer>
<name>sphericalResolution</name>
<label>Subdivisions</label>
<flag>-r</flag>
<longflag>--division</longflag>
<description>Number of subdivision for surface parameterization (4002 vertices for 20)</description>
<default>12</default>
<constraints>
<minimum>10</minimum>
<maximum>20</maximum>
</constraints>
</integer>
<integer>
<name>postDilationRadius</name>
<label>Dilation Radius after deformation</label>
<flag>-d</flag>
<longflag>--dilation</longflag>
<description>Radius of the structure element for dilation</description>
<default>0</default>
<constraints>
<minimum>0</minimum>
<maximum>4</maximum>
</constraints>
</integer>
</parameters>
<parameters advanced="true">
<label>Optional Output</label>
<description>Output for intermediate results.</description>
<image hidden="true">
<name>csfMemberShip</name>
<label>CSF membership function</label>
<longflag>--csf</longflag>
<description>Membership function of csf inside brain mask.</description>
<channel>output</channel>
<default>""</default>
</image>
<image hidden="true">
<name>GMMemberShip</name>
<label>Gray Matter membership function</label>
<flag>-g</flag>
<longflag>--gm</longflag>
<description>Membership function of gray matter inside brain mask.</description>
<channel>output</channel>
<default>""</default>
</image>
<image hidden="true">
<name>WMMemberShip</name>
<label>White Matter membership function</label>
<flag>-w</flag>
<longflag>--wm</longflag>
<description>Membership function of white matter inside brain mask.</description>
<channel>output</channel>
<default>""</default>
</image>
<image type="label" hidden="true">
<name>labelCombined</name>
<label>Combined hard segmentation</label>
<flag>-l</flag>
<longflag>--label</longflag>
<description>Hard segmentation of GM, WM, and CSF.</description>
<channel>output</channel>
<default>""</default>
</image>
</parameters>
</executable>