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dicom_to_nifti.xml
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dicom_to_nifti.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: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" xmlns:fileUtils="http://www.xnat.org/java/org.nrg.imagingtools.utils.FileUtils">
<name>DicomToNiftiCconverter</name>
<!--Should be Name of the pipeline XML file -->
<location>/home/vmuser/xnat_1_5_2/pipeline/mriconvert</location>
<!-- Filesystem path to the pipeline XML -->
<description>Demo pipeline created NIFTI files from the DICOM files and addes these files at SCAN level</description>
<documentation>
<authors>
<author>
<lastname>Mohana</lastname>
<firstname>Ramaratnam</firstname>
</author>
</authors>
<version>1</version>
<input-parameters>
<parameter>
<name>scanids</name>
<values>
<schemalink>xnat:imageSessionData/scans/scan/ID</schemalink>
</values>
<description>The scan ids of all the scans of the session</description>
</parameter>
<parameter>
<name>project</name>
<values>
<schemalink>xnat:imageSessionData/project</schemalink>
</values>
<description>The experiments project id</description>
</parameter>
<parameter>
<name>subject</name>
<values>
<schemalink>xnat:imageSessionData/subject_ID</schemalink>
</values>
<description>The experiments Subject</description>
</parameter>
<parameter>
<name>xnat_id</name>
<values>
<schemalink>xnat:imageSessionData/ID</schemalink>
</values>
<description>The experiments label</description>
</parameter>
<parameter>
<name>sessionId</name>
<values>
<schemalink>xnat:imageSessionData/label</schemalink>
</values>
<description>The experiments label</description>
</parameter>
<parameter>
<name>notify</name>
<values>
<csv>1</csv>
</values>
<description>Set the value to 1 if you want the pipeline to notify the user when complete. 0 otherwise</description>
</parameter>
</input-parameters>
</documentation>
<outputFileNamePrefix>^concat(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/',/Pipeline/name/text())^</outputFileNamePrefix>
<loop id="series" xpath="^/Pipeline/parameters/parameter[name='scanids']/values/list^"/>
<!-- Description of the Pipeilne -->
<parameters>
<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>
</parameters>
<steps>
<step id="0" description="Create a folder session folder" workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
<resource name="mkdir" location="commandlineTools" >
<!-- <argument id="p"/> -->
<argument id="dirname">
<value>NIFTI</value>
</argument>
</resource>
</step>
<step id="1" description="Create scan folders" workdirectory="^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI')^">
<resource name="mkdir" location="commandlineTools" >
<!-- <argument id="p"/> -->
<argument id="dirname">
<value>^PIPELINE_LOOPON(series)^</value>
</argument>
</resource>
</step>
<step id="0a" description="Create a folder session folder" workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
<resource name="mkdir" location="commandlineTools" >
<!-- <argument id="p"/> -->
<argument id="dirname">
<value>RAW</value>
</argument>
</resource>
</step>
<step id="1a" description="GET Scan DICOM DATA">
<resource name="XnatRestClient" location="xnat_tools">
<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="host">
<value>^/Pipeline/parameters/parameter[name='host']/values/unique/text()^</value>
</argument>
<argument id="method">
<value>GET</value>
</argument>
<argument id="remote">
<value>^concat('"/data/archive/projects/',/Pipeline/parameters/parameter[name='project']/values/unique/text(),'/subjects/',/Pipeline/parameters/parameter[name='subject']/values/unique/text(),'/experiments/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'/scans/ALL/resources/DICOM/files?format=zip&structure=legacy"')^</value>
</argument>
<argument id="redirect_output">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'.zip')^</value>
</argument>
</resource>
</step>
<step id="1b" description="Unzip the scan files" workdirectory="^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW')^">
<resource name="unzip" location="commandlineTools">
<argument id="source">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'.zip')^</value>
</argument>
<argument id="destination">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW')^</value>
</argument>
</resource>
</step>
<step id="2" description="Convert each series file into a 4d NIFTI file" >
<resource name="mcverter" location="mriconvert/resource">
<argument id="output">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI/',PIPELINE_LOOPON(series))^</value>
</argument>
<argument id="format">
<value>nifti</value>
</argument>
<argument id="nii"/>
<argument id="4dFile"/>
<argument id="input">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/SCANS/',PIPELINE_LOOPON(series),'/DICOM')^</value>
</argument>
</resource>
</step>
<step id="3" description="Upload files to XNAT" >
<resource name="XnatRestClient" location="xnat_tools">
<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="host">
<value>^/Pipeline/parameters/parameter[name='host']/values/unique/text()^</value>
</argument>
<argument id="method">
<value>PUT</value>
</argument>
<argument id="remote">
<value>^concat('"/data/archive/projects/',/Pipeline/parameters/parameter[name='project']/values/unique/text(),'/subjects/',/Pipeline/parameters/parameter[name='subject']/values/unique/text(),'/experiments/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'/scans/',PIPELINE_LOOPON(series),'resources/NIFTI/files/',PIPELINE_LOOPON(series),'.nii?format=NIFTI&content=NIFTI_RAW"')^</value>
</argument>
<argument id="local">
<value>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/NIFTI/',PIPELINE_LOOPON(series),'/*.nii')^</value>
</argument>
</resource>
</step>
<step id="END-Notify" description="Notify" precondition="^/Pipeline/parameters/parameter[name='notify']/values/unique/text()=1^">
<resource name="Notifier" location="notifications">
<argument id="to">
<value>^/Pipeline/parameters/parameter[name='useremail']/values/unique/text()^</value>
</argument>
<argument id="cc">
<value>^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^</value>
</argument>
<argument id="from">
<value>^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^</value>
</argument>
<argument id="subject">
<value>^concat(/Pipeline/parameters/parameter[name='xnatserver']/values/unique/text(), ' update: NIFTI files generated for ',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text() )^</value>
</argument>
<argument id="host">
<value>^/Pipeline/parameters/parameter[name='mailhost']/values/unique/text()^</value>
</argument>
<argument id="body">
<value>^concat('Dear ',/Pipeline/parameters/parameter[name='userfullname']/values/unique/text(),',<br> <p>', ' NIFTI files have been generated for ', /Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),' . Details of the session are available <a href="',/Pipeline/parameters/parameter[name='host']/values/unique/text(),'/app/action/DisplayItemAction/search_element/xnat:mrSessionData/search_field/xnat:mrSessionData.ID/search_value/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'">', ' here. </a> </p><br>', ' </p><br>', 'XNAT Team.')^
</value>
</argument>
</resource>
</step>
</steps>
</Pipeline>