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| − | # The main features of the project
| + | <big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Pipeline_Integration here]</font></big> |
| − | ## http://pipeline.loni.ucla.edu
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| − | # The main outstanding questions that must be answered before you can complete the project (or even start)
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| − | ## Pipeline -> Slicer3
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| − | ### Once the API for submission to Slicer3 is released, we can integrate it into the Pipeline.
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| − | ## Slicer3 -> Pipeline
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| − | ### Current Status
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| − | #### We have some code that allows any external application to start an instance of Pipeline and submit workflows.
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| − | #### Implement a JSON Interface to the pipeline that allows external applications to get a JSON parametric-description of submitted pipelines
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| − | #### Example usage: java -jar pipeline.jar -json MultiModalityRigidRegistration.module - The list of parameters in JSON format -
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| − | | |
| − | {"parameters":[
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"",
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| − | "class-type":"Command Line Option",
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| − | "name":"ResolutionLevel"
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| − | },
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"",
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| − | "class-type":"Command Line Option",
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| − | "name":"QualityLevel"
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| − | },
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"input",
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| − | "class-type":"File",
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| − | "name":"FixedImage"
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| − | },
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"output",
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| − | "class-type":"File",
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| − | "name":"OutputTransform"
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| − | },
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"input",
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| − | "class-type":"File",
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| − | "name":"MovingImage"
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| − | },
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| − | {
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| − | "phantom":"false",
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| − | "optional":"false",
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| − | "connection-type":"input",
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| − | "class-type":"File",
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| − | "name":"InputTransform"
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| − | }
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| − | ]
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| − | }
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| − | | |
| − | # This JSON description can be then used to bind values to parameters and then submit the pipeline for
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| − | | |
| − | execution -
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| − | | |
| − | # The XML representation is given below:
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| − | | |
| − |
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| − | <?xml version="1.0" encoding="UTF-8"?>
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| − | <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#">
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| − | <owl:Ontology>
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| − | <owl:versionInfo><![CDATA[20050412]]></owl:versionInfo>
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| − | <rdfs:label locale="en" />
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| − | <rdfs:comment locale="en" />
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| − | </owl:Ontology>
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| − | <FunctionPipeline rdf:ID="1118265959469">
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| − | <rdfs:label locale="en"><![CDATA[MultiModalityRigidRegistration pipeline function]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[MultiModalityRigidRegistration (Programmers Week)]]></rdfs:comment>
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| − | <Assign rdf:ID="11182659594690">
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| − | <owl:allValuesFrom rdf:resource="1118265959620" />
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| − | <rdfs:label locale="en"><![CDATA[11182659594690]]></rdfs:label>
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| − | </Assign>
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| − | <GUI>
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| − | <rdfs:label locale="en" />
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| − | <rdfs:comment locale="en" />
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| − | </GUI>
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| − | </FunctionPipeline>
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| − | <Module rdf:ID="1118265959469:1118265959586" rdf:resource="1118265959469">
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| − | <rdfs:label locale="en"><![CDATA[MultiModalityRigidRegistration pipeline]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[MultiModalityRigidRegistration (Programmers Week)]]></rdfs:comment>
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| − | <Module rdf:ID="1118265959620:1118265959625" rdf:resource="11182659594690">
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| − | <rdfs:label locale="en"><![CDATA[MultiModalityRigidRegistration]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[MultiModalityRigidRegistration (Programmers Week)]]></rdfs:comment>
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| − | <GUI x="196" y="171">
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| − | <rdfs:label locale="en" />
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| − | <rdfs:comment locale="en" />
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| − | </GUI>
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| − | <Assign rdf:resource="Parameter1118266141102">
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| − | <owl:allValuesFrom rdf:resource="File:1118266118686" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | <Assign rdf:resource="Parameter1118266282720">
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| − | <owl:allValuesFrom rdf:resource="File:1118266266201" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | <Assign rdf:resource="Parameter1118266397117">
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| − | <owl:allValuesFrom rdf:resource="File:1118266372629" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | <Assign rdf:resource="Parameter1118266521616">
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| − | <owl:allValuesFrom rdf:resource="CommandLineOption:1118266435955" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | <Assign rdf:resource="Parameter1118266541544">
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| − | <owl:allValuesFrom rdf:resource="CommandLineOption:1118266461834" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | <Assign rdf:resource="Parameter1118266740529">
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| − | <owl:allValuesFrom rdf:resource="File:1118266713458" />
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| − | <rdfs:label locale="en" />
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| − | </Assign>
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| − | </Module>
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| − | </Module>
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| − | <ExecutableFile rdf:ID="1118265959620" url="pipeline://localhost//home/jrajendi/ProgrammersWeek/ItkGridPipeline/testdir/grid-reg/MultiModalityRigidRegistration">
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| − | <rdfs:label locale="en"><![CDATA[MultiModalityRigidRegistration function]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[MultiModalityRigidRegistration (Programmers Week)]]></rdfs:comment>
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| − | <GUI>
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| − | <rdfs:label locale="en" />
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| − | <rdfs:comment locale="en" />
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| − | </GUI>
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| − | <Parameter rdf:ID="Parameter1118266141102" connectionType="input">
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| − | <rdfs:label locale="en"><![CDATA[FixedImage]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[Fixed Image parameter]]></rdfs:comment>
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| − | <rdf:type rdf:resource="File" />
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| − | </Parameter>
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| − | <Parameter rdf:ID="Parameter1118266282720" connectionType="input">
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| − | <rdfs:label locale="en"><![CDATA[MovingImage]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[moving image parameter]]></rdfs:comment>
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| − | <rdf:type rdf:resource="File" />
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| − | </Parameter>
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| − | <Parameter rdf:ID="Parameter1118266397117" connectionType="input">
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| − | <rdfs:label locale="en"><![CDATA[InputTransform]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[input transform parameter]]></rdfs:comment>
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| − | <rdf:type rdf:resource="File" />
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| − | </Parameter>
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| − | <Parameter rdf:ID="Parameter1118266521616" connectionType="">
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| − | <rdfs:label locale="en"><![CDATA[ResolutionLevel]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[resolutionlevel parameter]]></rdfs:comment>
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| − | <rdf:type rdf:resource="CommandLineOption" />
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| − | </Parameter>
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| − | <Parameter rdf:ID="Parameter1118266541544" connectionType="">
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| − | <rdfs:label locale="en"><![CDATA[QualityLevel]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[Quality level]]></rdfs:comment>
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| − | <rdf:type rdf:resource="CommandLineOption" />
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| − | </Parameter>
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| − | <Parameter rdf:ID="Parameter1118266740529" connectionType="output">
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| − | <rdfs:label locale="en"><![CDATA[OutputTransform]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[output transform file]]></rdfs:comment>
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| − | <rdf:type rdf:resource="File" />
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| − | </Parameter>
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| − | </ExecutableFile>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266044377">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[pipeline://localhost//home/jrajendi/ProgrammersWeek/ItkGridPipeline/testdir/grid-reg/]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[Input Directory]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[input directory for images and input configuration files]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266073584">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[reg.nhdr]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[Fixed Image Filename]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[reg.nhdr filename]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <File rdf:ID="File:1118266118686">
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| − | <Values>
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| − | <Value>
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| − | <string rdf:resource="CommandLineOption:1118266044377" />
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| − | <string rdf:resource="CommandLineOption:1118266073584" />
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[FixedImage]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[fixed image variable]]></rdfs:comment>
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| − | </File>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266234482">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[mrt.nhdr]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[Moving Image Filename]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[filename for moving image input]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <File rdf:ID="File:1118266266201">
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| − | <Values>
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| − | <Value>
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| − | <string rdf:resource="CommandLineOption:1118266044377" />
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| − | <string rdf:resource="CommandLineOption:1118266234482" />
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[MovingImage]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[Moving image variable]]></rdfs:comment>
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| − | </File>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266341295">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[xformIN]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[InputTransform Filename]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[Input Transformation Filename]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <File rdf:ID="File:1118266372629">
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| − | <Values>
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| − | <Value>
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| − | <string rdf:resource="CommandLineOption:1118266044377" />
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| − | <string rdf:resource="CommandLineOption:1118266341295" />
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[InputTransform]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[input transformation variable]]></rdfs:comment>
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| − | </File>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266435955">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[2]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[ResolutionLevel]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[resolution levels {1, 2, 3}]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266461834">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[1]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[QualityLevel]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[quality levels {1,2}]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266576527">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[xformOUT]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[OuputTransform Filename]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[output transform filename]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <CommandLineOption rdf:ID="CommandLineOption:1118266669340">
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| − | <Values>
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| − | <Value>
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| − | <string><![CDATA[pipeline://localhost//home/jrajendi/ProgrammersWeek/ItkGridPipeline/testdir/grid-reg/refinedmodule/]]></string>
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[Output Directory]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[output directory for outputTransformfile]]></rdfs:comment>
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| − | </CommandLineOption>
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| − | <File rdf:ID="File:1118266713458">
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| − | <Values>
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| − | <Value>
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| − | <string rdf:resource="CommandLineOption:1118266669340" />
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| − | <string rdf:resource="CommandLineOption:1118266576527" />
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| − | </Value>
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| − | </Values>
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| − | <rdfs:label locale="en"><![CDATA[OutputTransform]]></rdfs:label>
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| − | <rdfs:comment locale="en"><![CDATA[output transform file]]></rdfs:comment>
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| − | </File>
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| − | </rdf:RDF>
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| − | | |
| − | <br />
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| − | | |
| − | # To start a pipeline on the commandline with parameters:
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| − | | |
| − | java -jar pipeline.client.jar -batch -module=MultiModalityRigidRegistration.module -parameter:Paramter_1=Value_1 -parameter:Parameter_2=Value_2
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| − | | |
| − | '''Team Members'''<nowiki>: </nowiki>
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| − | | |
| − | * Michael Pan - UCLA
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| − | * Jagadeeswaran Rajendiran - UCLA
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