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XNAT2BIDS2.xml
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XNAT2BIDS2.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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>XNAT2BIDS2</name>
<location>bids2</location>
<description>Pipeline creates BIDS2 output from DICOM files using XNAT
pipeline engine.</description>
<documentation>
<authors>
<author>
<lastname>Lipinski</lastname>
<firstname>Kamil</firstname>
<contact>
<email>[email protected]</email>
</contact>
</author>
</authors>
<version>20170901</version>
<input-parameters>
<parameter>
<name>scanids</name>
<values>
<schemalink>xnat:imageSessionData/scans/scan/ID</schemalink>
</values>
<description>Scan ids of all the scans of the session</description>
</parameter>
<parameter>
<name>xnat_id</name>
<values>
<schemalink>xnat:imageSessionData/ID</schemalink>
</values>
<description>XNAT ID (Accession Number) of the session</description>
</parameter>
<parameter>
<name>sessionId</name>
<values>
<schemalink>xnat:imageSessionData/label</schemalink>
</values>
<description>Session label</description>
</parameter>
<parameter>
<name>project</name>
<values>
<schemalink>xnat:imageSessionData/project</schemalink>
</values>
<description>Project ID</description>
</parameter>
<parameter>
<name>subject</name>
<values>
<schemalink>xnat:imageSessionData/subject_ID</schemalink>
</values>
<description>Subject ID</description>
</parameter>
<parameter>
<name>sublabel</name>
<values>
<csv></csv>
</values>
<description>Subject ID</description>
</parameter>
</input-parameters>
</documentation>
<outputFileNamePrefix>^concat(/Pipeline/parameters/parameter[name='logdir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='label']/values/unique/text())^
</outputFileNamePrefix>
<loop id="series"
xpath="^/Pipeline/parameters/parameter[name='scanids']/values/list^" />
<parameters>
<parameter>
<name>sub</name>
<values>
<unique>^fileUtils:GetColumn(/Pipeline/parameters/parameter[name='host']/values/unique/text(),/Pipeline/parameters/parameter[name='user']/values/unique/text(),/Pipeline/parameters/parameter[name='pwd']/values/unique/text(),
concat('/data/subjects/',/Pipeline/parameters/parameter[name='subject']/values/unique/text(),'?handler=values&format=json&columns=label'),'label')^
</unique>
</values>
</parameter>
<parameter>
<name>finallabel</name>
<values>
<unique>^if(
if(boolean(/Pipeline/parameters/parameter[name='sublabel']))
then
/Pipeline/parameters/parameter[name='sublabel']/values/unique/text()!=''
else false() )
then
/Pipeline/parameters/parameter[name='sublabel']/values/unique/text()
else
/Pipeline/parameters/parameter[name='sub']/values/unique/text()^
</unique>
</values>
</parameter>
<parameter>
<name>workdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='builddir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='finallabel']/values/unique/text())^
</unique>
</values>
</parameter>
<parameter>
<name>logdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/LOGS')^
</unique>
</values>
</parameter>
<parameter>
<name>rawdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/RAW')^
</unique>
</values>
</parameter>
<parameter>
<name>bidsdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/sub-',/Pipeline/parameters/parameter[name='finallabel']/values/unique/text())^
</unique>
</values>
</parameter>
<parameter>
<name>tempdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/TEMP')^
</unique>
</values>
</parameter>
<parameter>
<name>anatdir</name>
<values>
<unique>^concat(/Pipeline/parameters/parameter[name='bidsdir']/values/unique/text(),'/anat')^
</unique>
</values>
</parameter>
<parameter>
<name>resolved_host</name>
<values>
<unique>^if(boolean(/Pipeline/parameters/parameter[name='aliasHost']))
then
/Pipeline/parameters/parameter[name='aliasHost']/values/unique/text()
else
/Pipeline/parameters/parameter[name='host']/values/unique/text()^
</unique>
</values>
</parameter>
<parameter>
<name>email_subject</name>
<values>
<unique>^concat('XNAT update: BIDS output generated for
',/Pipeline/parameters/parameter[name='label']/values/unique/text())^
</unique>
</values>
</parameter>
<parameter>
<name>email_body</name>
<values>
<unique>^concat('Dear
',/Pipeline/parameters/parameter[name='userfullname']/values/unique/text(),',<br>
<p>BIDS output have been generated for ',
/Pipeline/parameters/parameter[name='label']/values/unique/text(),'.
Details <a
href="',/Pipeline/parameters/parameter[name='resolved_host']/values/unique/text(),'/data/experiments',/Pipeline/parameters/parameter[name='id']/values/unique/text(),'?format=html">here.</a>
</p><br></p><br>XNAT Team.')^</unique>
</values>
</parameter>
</parameters>
<steps>
<step id="mkdir_raw" description="Create RAW folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^/Pipeline/parameters/parameter[name='rawdir']/values/unique/text()^
</value>
</argument>
</resource>
</step>
<step id="mkdir_temp" description="Create TEMP folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^/Pipeline/parameters/parameter[name='tempdir']/values/unique/text()^
</value>
</argument>
</resource>
</step>
<step id="mkdir_bids" description="Create BIDS folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^/Pipeline/parameters/parameter[name='bidsdir']/values/unique/text()^
</value>
</argument>
</resource>
</step>
<step id="mkdir_anat" description="Create Anatomical folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^/Pipeline/parameters/parameter[name='anatdir']/values/unique/text()^
</value>
</argument>
</resource>
</step>
<step id="mkdir_func" description="Create Functional folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^concat(/Pipeline/parameters/parameter[name='bidsdir']/values/unique/text(),'/func')^
</value>
</argument>
</resource>
</step>
<step id="mkdir_dti" description="Create dwi folder">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^concat(/Pipeline/parameters/parameter[name='bidsdir']/values/unique/text(),'/dwi')^
</value>
</argument>
</resource>
</step>
<step id="mkdir_raw_series" description="Create folder for each series in RAW subfolder"
workdirectory="^/Pipeline/parameters/parameter[name='rawdir']/values/unique/text()^">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^PIPELINE_LOOPON(series)^</value>
</argument>
</resource>
</step>
<step id="mkdir_bids_outp" description="Create folder for each series in output dir"
workdirectory="^/Pipeline/parameters/parameter[name='tempdir']/values/unique/text()^">
<resource name="mkdir" location="commandlineTools">
<argument id="dirname">
<value>^PIPELINE_LOOPON(series)^</value>
</argument>
</resource>
</step>
<step id="get" description="Download scan DICOMs"
workdirectory="^concat(/Pipeline/parameters/parameter[name='rawdir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^">
<resource name="XnatDataClient" location="xnat_tools">
<argument id="sessionId">
<value>^fileUtils:getJSESSION('DUMMY')^</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="absolutePath" />
<argument id="batch" />
<argument id="method">
<value>GET</value>
</argument>
<argument id="remote">
<value>^concat('"',/Pipeline/parameters/parameter[name='resolved_host']/values/unique/text(),'/data/experiments/',/Pipeline/parameters/parameter[name='id']/values/unique/text(),'/scans/',PIPELINE_LOOPON(series),'/resources/DICOM/files"')^
</value>
</argument>
</resource>
</step>
<step id="conversion"
description="Convert each DICOM series into a 4d NIFTI file and create sidecar json">
<resource name="dcm2niix" location="bids2/resources">
<argument id="Compression">
<value>y</value>
</argument>
<argument id="Merge">
<value>y</value>
</argument>
<argument id="Jsons">
<value>y</value>
</argument>
<argument id="Output">
<value>^concat(/Pipeline/parameters/parameter[name='tempdir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^
</value>
</argument>
<argument id="input">
<value>^concat(/Pipeline/parameters/parameter[name='rawdir']/values/unique/text(),'/',PIPELINE_LOOPON(series))^
</value>
</argument>
</resource>
</step>
<step id="move" description="Places the files in the right subfolders"
workdirectory="^/Pipeline/parameters/parameter[name='tempdir']/values/unique/text()^">
<resource name="ordnung" location="bids2/resources">
<argument id="input">
<value>^/Pipeline/parameters/parameter[name='tempdir']/values/unique/text()^
</value>
</argument>
<argument id="label">
<value>^/Pipeline/parameters/parameter[name='finallabel']/values/unique/text()^
</value>
</argument>
<argument id="output">
<value>^/Pipeline/parameters/parameter[name='bidsdir']/values/unique/text()^
</value>
</argument>
<argument id="session_label">
<value>^/Pipeline/parameters/parameter[name='sessionId']/values/unique/text()^
</value>
</argument>
</resource>
</step>
<step id="compress" description="compress"
workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
<resource name="zip" location="commandlineTools">
<argument id="recursive">
</argument>
<argument id="archive">
<value>^concat(/Pipeline/parameters/parameter[name='finallabel']/values/unique/text(),'.zip')^
</value>
</argument>
<argument id="folder">
<value>^concat('sub-',/Pipeline/parameters/parameter[name='finallabel']/values/unique/text(),'/')^
</value>
</argument>
</resource>
</step>
<step id="UPLOAD" description="Upload compressed package">
<resource name="XnatDataClient" location="xnat_tools">
<argument id="sessionId">
<value>^fileUtils:getJSESSION('DUMMY')^</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="method">
<value>PUT</value>
</argument>
<argument id="remote">
<value>^concat('"',/Pipeline/parameters/parameter[name='resolved_host']/values/unique/text(),'/data/experiments/',/Pipeline/parameters/parameter[name='id']/values/unique/text(),'/resources/bids/files?overwrite=true&format=zip&reference=',/Pipeline/parameters/parameter[name='workdir']/values/unique/text(),'/',/Pipeline/parameters/parameter[name='finallabel']/values/unique/text(),'.zip','"')^
</value>
</argument>
</resource>
</step>
<step id="END-Notify" description="Notify">
<resource name="Notifier" location="notifications">
<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="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>^/Pipeline/parameters/parameter[name='email_subject']/values/unique/text()^
</value>
</argument>
<argument id="host">
<value>^/Pipeline/parameters/parameter[name='mailhost']/values/unique/text()^
</value>
</argument>
<argument id="body">
<value>^/Pipeline/parameters/parameter[name='email_body']/values/unique/text()^
</value>
</argument>
</resource>
</step>
</steps>
</Pipeline>