biswebnode/bin/bw_slicebiascorrect.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>Bias Field Correct</title>
	<description>Performs slice-based intensity inhomogeneity (bias field) correction on an image to correct for acquisition artifacts. This includes B1 inhomogeneity correction for MRI, or attenuation issues in microscopy.</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Zach Saltzman and Xenios Papademetris</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>
		<string-enumeration>
			<name>Axis</name>
			<label>Axis</label>
			<description>Which axis to correct along ('x', 'y', 'z', 'triple')</description>
			<longflag>--axis</longflag>
			<default>z</default>
			<element>x</element>
			<element>y</element>
			<element>z</element>
			<element>triple</element>
		</string-enumeration>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<double>
			<name>Threshold</name>
			<label>Threshold</label>
			<description>This sets the threshold (percentage of max intensity), below which the image is masked</description>
			<longflag>--threshold</longflag>
			<default>0.05</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>0.5</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>Return Bias Field</name>
			<label>Return Bias Field</label>
			<description>If false (default), this returns the the corrected image. Otherwise (true) it returns the estimated bias field.</description>
			<longflag>--returnbiasfield</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>Input Image</name>
			<label>Input Image</label>
			<description>The filename for the image to be processed</description>
			<longflag>--input</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>The output image filename</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>