biswebnode/bin/bw_motioncorrection.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>Motion Correction</title>
	<description>Runs motion correction</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Michelle Lim</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>Levels</name>
			<label>Levels</label>
			<description>Number of levels in multiresolution optimization</description>
			<longflag>--levels</longflag>
			<default>3</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>4</maximum>
			</constraints>
		</integer>
		<integer>
			<name>Iterations</name>
			<label>Iterations</label>
			<description>Number of iterations (per level and step)</description>
			<longflag>--iterations</longflag>
			<default>32</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>32</maximum>
			</constraints>
		</integer>
		<double>
			<name>Resolution</name>
			<label>Resolution</label>
			<description>Factor to reduce the resolution prior to registration</description>
			<longflag>--resolution</longflag>
			<default>1.01</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>5</maximum>
			</constraints>
		</double>
		<integer>
			<name>Reference Frame Number</name>
			<label>Reference Frame Number</label>
			<description>Frame number of reference image used for linear registration</description>
			<longflag>--refno</longflag>
			<default>0</default>
		</integer>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Reslice</name>
			<label>Reslice</label>
			<description>If true, also output a resliced targed image using the current transform</description>
			<longflag>--doreslice</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>Normalize</name>
			<label>Normalize</label>
			<description>If true, normalize input intensities by saturating using cumulative histogram</description>
			<longflag>--norm</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<integer>
			<name>Int Scale</name>
			<label>Int Scale</label>
			<description>Determines the intensity scaling post image normalization</description>
			<longflag>--intscale</longflag>
			<default>1</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>4</maximum>
			</constraints>
		</integer>
		<string-enumeration>
			<name>Number of Bins</name>
			<label>Number of Bins</label>
			<description>Number of bins in joint histogram</description>
			<longflag>--numbins</longflag>
			<default>1024</default>
			<element>16</element>
			<element>32</element>
			<element>64</element>
			<element>128</element>
			<element>256</element>
			<element>512</element>
			<element>1024</element>
		</string-enumeration>
		<double>
			<name>Smoothing</name>
			<label>Smoothing</label>
			<description>Amount of image smoothing to perform</description>
			<longflag>--imagesmoothing</longflag>
			<default>1</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>4</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>Metric</name>
			<label>Metric</label>
			<description>Metric to compare registration</description>
			<longflag>--metric</longflag>
			<default>CC</default>
			<element>SSD</element>
			<element>CC</element>
			<element>MI</element>
			<element>NMI</element>
		</string-enumeration>
		<string-enumeration>
			<name>Optimization</name>
			<label>Optimization</label>
			<description>Optimization Method</description>
			<longflag>--optimization</longflag>
			<default>HillClimb</default>
			<element>HillClimb</element>
			<element>GradientDescent</element>
			<element>ConjugateGradient</element>
		</string-enumeration>
		<double>
			<name>Step Size</name>
			<label>Step Size</label>
			<description>Step size for gradient computation</description>
			<longflag>--stepsize</longflag>
			<default>0.125</default>
			<constraints>
				<minimum>0.125</minimum>
				<maximum>4</maximum>
			</constraints>
		</double>
		<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>
		<integer>
			<name>Steps</name>
			<label>Steps</label>
			<description>Number of steps in multiresolution optimization</description>
			<longflag>--steps</longflag>
			<default>4</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>4</maximum>
			</constraints>
		</integer>
		<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>Reference Image</name>
			<label>Reference Image</label>
			<description>The reference image</description>
			<longflag>--reference</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Target Image</name>
			<label>Target Image</label>
			<description>The image to register</description>
			<longflag>--target</longflag>
    			<channel>input</channel>
		</image>
		<file>
			<name>Initial Xform</name>
			<label>Initial Xform</label>
			<description>The initial transformation (optional)</description>
			<longflag>--initial</longflag>
    			<channel>input</channel>
		</file>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<file>
			<name>Output Transformation</name>
			<label>Output Transformation</label>
			<description>The output transformation</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</file>
		<image fileExtensions=".nii.gz,.nii">
			<name>Resliced Image</name>
			<label>Resliced Image</label>
			<description>The resliced image</description>
			<longflag>--resliced</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>