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Arash_DWIpreprocessing.xml
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Arash_DWIpreprocessing.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- edited with XMLSPY v2004 rel. 3 U (http://www.xmlspy.com) by Mohana Ramaratnam (Washington University) -->
<Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:fileUtils="http://www.xnat.org/java/org.nrg.imagingtools.utils.FileUtils"
xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://nrg.wustl.edu/pipeline ..\schema\pipeline.xsd">
<name>Arash_DWIpreprocessing</name>
<!--Should be Name of the pipeline XML file -->
<location>/data/xnat/pipeline/MCWpipelines/Arash/Arash_DWIpreprocessing</location>
<!-- Filesystem path to the pipeline XML -->
<description>Launches the DWI preprocessing pipeline on the cluster.</description>
<documentation>
<authors>
<author>
<lastname>Zakszewski</lastname>
<firstname>Liz</firstname>
</author>
</authors>
<version>1</version>
<input-parameters>
<parameter>
<name>subject</name>
<values>
<schemalink>xnat:imageSessionData/subject_ID</schemalink>
</values>
<description>Subject ID</description>
</parameter>
<parameter>
<name>subjName</name>
<values>
<schemalink>xnat:imageSessionData/dcmPatientName</schemalink>
</values>
<description>Subject name from DICOM</description>
</parameter>
<parameter>
<name>sessionDate</name>
<values>
<schemalink>xnat:imageSessionData/date</schemalink>
</values>
<description>The date of acquisition for the session</description>
</parameter>
<parameter>
<name>sessionId</name>
<values><schemalink>xnat:imageSessionData/label</schemalink></values>
<description>The session id of the session</description>
</parameter>
</input-parameters>
</documentation>
<outputFileNamePrefix>^concat(/Pipeline/parameters/parameter[name='logdir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name="label"]/values/unique/text())^</outputFileNamePrefix>
<parameters>
<parameter>
<name>xnat_id</name>
<values>
<unique>^Pipeline/parameters/parameter[name="id"]/values/unique/text()^</unique>
</values>
<description>The XNAT ID (Accession Number) of the session</description>
</parameter>
<parameter>
<name>sessionId</name>
<values>
<unique>^Pipeline/parameters/parameter[name="label"]/values/unique/text()^</unique>
</values>
<description>The session id of the session</description>
</parameter>
<parameter>
<name>workdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text())^</unique>
</values>
</parameter>
<parameter>
<name>logdir</name>
<values>
<unique>/data/xnat/pipeline/MCWlogs</unique>
</values>
</parameter>
</parameters>
<!-- Description of the Pipeilne -->
<steps>
<step description="SpawnCluster" id="Cluster">
<resource location="MCWdescriptors" name="GE_DWI_Preproc_SwitchUser">
<argument id="BaseDir">
<value>"/data/xnat/remotebuild/"</value>
</argument>
<argument id="user">
<value>^/Pipeline/parameters/parameter[name='user']/values/unique/text()^</value>
</argument>
<argument id="password">
<value>^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^</value>
</argument>
<argument id="NoTopup"/>
<argument id="addr"><value>^/Pipeline/parameters/parameter[name='host']/values/unique/text()^</value></argument>
<argument id="proj"><value>^/Pipeline/parameters/parameter[name='project']/values/unique/text()^</value></argument>
<argument id="exp"><value>^/Pipeline/parameters/parameter[name='sessionId']/values/unique/text()^</value></argument>
<argument id="subj"><value>^/Pipeline/parameters/parameter[name='subject']/values/unique/text()^</value></argument>
<argument id="supDir">
<value>"/data/xnat/pipeline/MCWbin/ClusterJobs/GE_DWI_Preprocess/"</value>
</argument>
<argument id="AP"><value>'DTI 2mm'</value></argument>
<!-- <argument id="PA"><value>'SB DTI MCW P/A'</value></argument>
<argument id="Verbose"/> -->
<argument id="AcFile"><value>'acqparams.txt'</value></argument>
</resource>
</step>
</steps>
</Pipeline>
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