biswebnode/bin/bw_motionreslice.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 Reslices data</title>
	<description>Reslices following motion correction</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>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>Interpolation</name>
			<label>Interpolation</label>
			<description>Which type of interpolation to use (3 = cubic, 1 = linear, 0 = nearest-neighbor)</description>
			<longflag>--interpolation</longflag>
			<default>3</default>
			<element>0</element>
			<element>1</element>
			<element>3</element>
		</string-enumeration>
		<double>
			<name>Res factor</name>
			<label>Res factor</label>
			<description>The amount to downsample the reference by</description>
			<longflag>--res</longflag>
			<default>2</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>4</maximum>
			</constraints>
		</double>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>Force Float</name>
			<label>Force Float</label>
			<description>If true force output to float</description>
			<longflag>--forcefloat</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<double>
			<name>Fill Value</name>
			<label>Fill Value</label>
			<description>Value to use for outside the image</description>
			<longflag>--backgroundvalue</longflag>
			<default>0</default>
		</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>
		<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>Image to Reslice</name>
			<label>Image to Reslice</label>
			<description>Load the image to reslice</description>
			<longflag>--input</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Reference Image</name>
			<label>Reference Image</label>
			<description>Load the reference image (if not specified use input)</description>
			<longflag>--reference</longflag>
    			<channel>input</channel>
		</image>
		<file>
			<name>Reslice Transform (Atlas->Ref)</name>
			<label>Reslice Transform (Atlas->Ref)</label>
			<description>Load the transformation used to reslice the image</description>
			<longflag>--xform</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>Transformation 2 (Ref->Conv)</name>
			<label>Transformation 2 (Ref->Conv)</label>
			<description>The second transformation to combine with first</description>
			<longflag>--xform2</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>Transformation 3 (Conv->EPI)</name>
			<label>Transformation 3 (Conv->EPI)</label>
			<description>The third transformation to combine with first and second</description>
			<longflag>--xform3</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>Motion Correction Collection</name>
			<label>Motion Correction Collection</label>
			<description>The output of the motion Correction</description>
			<longflag>--motionparam</longflag>
    			<channel>input</channel>
		</file>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output Image</name>
			<label>Output Image</label>
			<description>Save the motion resliced image</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>