biswebnode/bin/bw_individualizedparcellation.xml

A node.js implementation of BioImage Suite Web command line tools in Javascript and WebAssembly

<?xml version="1.0" encoding="utf-8"?>
<executable>
	<category>BisWEB</category>
	<title>Compute Individualized parcellation</title>
	<description>Calculates the individualized parcellation starting from an original (group) parcellation</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Mehraveh Salehi</contributor>

<acknowledgements>Funding for this work was provided by the NIH Brain Initiative under grant R24 MH114805.</acknowledgements>
	<parameters>
		<label>Standard</label>
		<description>Standard Parameters</description>
		<integer>
			<name>Num Regions</name>
			<label>Num Regions</label>
			<description>The number of regions in the original (group) parcellation</description>
			<longflag>--numregions</longflag>
			<default>268</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>5000</maximum>
			</constraints>
		</integer>
		<double>
			<name>Smoothing</name>
			<label>Smoothing</label>
			<description>Kernel size [mm] of FWHM filter size</description>
			<longflag>--smooth</longflag>
			<default>4</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>20</maximum>
			</constraints>
		</double>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Save Exemplars?</name>
			<label>Save Exemplars?</label>
			<description>Saves exemplars in second frame</description>
			<longflag>--saveexemplars</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>Debug</name>
			<label>Debug</label>
			<description>Toggles debug logging</description>
			<longflag>--debug</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>SlicerProgress</name>
			<label>SlicerProgress</label>
			<description>Enables progress xml outputs for Slicer</description>
			<longflag>--slicerprogress</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
	</parameters>
	<parameters>
		<label>Inputs</label>
		<description>Input Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>fMRI Image</name>
			<label>fMRI Image</label>
			<description>The fMRI image to parcellate</description>
			<longflag>--fmri</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Input Parcellation</name>
			<label>Input Parcellation</label>
			<description>The original (group) parcellation to individualize</description>
			<longflag>--parc</longflag>
    			<channel>input</channel>
		</image>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output Image</name>
			<label>Output Image</label>
			<description>Output: the individualized parcellation</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>