<?xml version="1.0" encoding="utf-8"?>

<executable>

<category>vtkSurfaces</category>

<title>ExtractLabelSurfaces</title>

<description>ExtractLabelSurfaces is a tool which extracted labels surfaces from a surface containing labels</description>

<version>1.0.4</version>

<contributor>Danaele Puechmaille, Francois Budin, Juan Carlos Prieto, Martin Styner, Adrien Boucaud</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, Grants U01 MH070890 - U54 HD079124 - R01 MH091351.]]></acknowledgements>

<parameters>

<label>Input</label>

<description>Input parameters</description>

<boolean>

<name>overlapping</name>

<longflag>overlapping</longflag>

<label>overlapping</label>

<default>false</default>

<description>Reconstruct label surfaces with overlapping </description>

</boolean>

<boolean>

<name>createSurfaceLabelFiles</name>

<longflag>createSurfaceLabelFiles</longflag>

<label>Create Surface Label Files</label>

<default>false</default>

<description>Create surfaces corresponding to each label : required flags --labelNumberInfo and --vtkFile. You can specified a prefix for identify surfaces files (for exemple : lh or rh).</description>

</boolean>

<boolean>

<name>extractPointData</name>

<longflag>extractPointData</longflag>

<label>Extract Point Data</label>

<default>false</default>

<description>Extract Point Data from the vtk file containing labels : required flags --vtklabelFile --arrayName/-a and --labelNameInfo </description>

</boolean>

<boolean>

<name>useTranslationTable</name>

<longflag>useTranslationTable</longflag>

<label>useTranslationTable</label>

<default>false</default>

<description>Find label filename with a translation table</description>

</boolean>

<boolean>

<name>translateToLabelNumber</name>

<longflag>translateToLabelNumber</longflag>

<label>Translate To Label Number</label>

<default>false</default>

<description>Translate labelNameInformation file to labelNumberInformation file : required flags --labelNameInfo and --labelNumberInfo. If you add a Translation table then you need to specified flags --useTable and --labelTranslationTable</description>

</boolean>

<geometry fileExtensions="vtk" multiple="false" >

<name>vtkFile</name>

<label>VTK File</label>

<longflag>vtkFile</longflag>

<description>Surface without label information from which we extract the different labeled surfaces ( myfile.vtk )</description>

</geometry>

<geometry fileExtensions="vtk" multiple="false" >

<name>vtkLabelFile</name>

<label>VTK label File</label>

<longflag>vtkLabelFile</longflag>

<description>Surface with labels information ( myfile_withLabel.vtk )</description>

</geometry>

<string>

<name>arrayName</name>

<label>Array Name</label>

<flag>a</flag>

<longflag>arrayName</longflag>

<description>Array name containing label information</description>

</string>

<string>

<name>ignoreLabel</name>

<label>ignoreLabel</label>

<flag>i</flag>

<longflag>ignoreLabel</longflag>

<default></default>

<description>Ignore the label Name specify - this label won't be created (ex : -i "0 0 0"). MUST BE USE WITH OPTION --useTranslationTable AND --labelTranslationTable</description>

</string>

<string>

<name>prefix</name>

<label>prefix</label>

<flag>p</flag>

<longflag>prefix</longflag>

<description>Prefix added in names of each output files </description>

</string>

<file fileExtensions="txt" >

<name >labelTranslationTable</name>

<label>Translation Table for labelNumber</label>

<longflag>labelTranslationTable</longflag>

<description>Table containing label number for each label name</description>

</file>

</parameters>

<parameters>

<label>IO</label>

<description>Input/Output parameters</description>

<file fileExtensions="txt" >

<name >labelNameInfo</name>

<label>List of label information</label>

<longflag>labelNameInfo</longflag>

<description>List containing label information by name. If 'extractPointData' is used, this file is generated.</description>

</file>

<file fileExtensions="txt" >

<name >labelNumberInfo</name>

<label>Load label info list by number </label>

<longflag>labelNumberInfo</longflag>

<description>List containing label information by number in accordance with a Translation table (--useTranslationTable) or not. </description>

</file>

</parameters>

<parameters>

<label>Output</label>

<description>Output parameters</description>

<directory>

<name >outputSurfaceDirectory</name>

<label>Ouput directory when '--createSurfaceLabelFiles' is used</label>

<longflag>outputSurfaceDirectory</longflag>

<description>Directory used to create the surfaces</description>

<default>labelSurfaces</default>

</directory>

</parameters>

</executable>