Deep Project Management with XNAT
Vanderbilt University
2013-08-20
Benjamin Yvernault,
Bennett Landman, Brian Boyd,
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Requirements
At this point, you should know how to :
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Register and Log in to XNAT
See your projects and join projects
Create project / sharing data
Manage access permissions
Browse data and view image previews
Search for projects, subjects, and data
Download imaging data, processed, and stored meta-data
Delete scans / sessions / projects
Use the Pre-Archive
Upload scans through DicomBrowser
Quality Assurance
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Set up your computer
Xnatsetup (basic) will on your computer :
 Install Python package to run the command tools :
 Instructions on the wiki
 Install lxml and httplib2 using easy_install or pip
 Install Pyxnat from a git version :
git clone git://github.com/sburns/PyCap.git PyCap
cd PyCap
python setup.py install
 Set up your .bashrc or .profile :
Remember!
 Set up the XNAT variables :
export XNAT_USER = bob (your xnat username)
export XNAT_PASS = bob (your xnat password)
export XNAT_HOST = http://xnat.vanderbilt.edu/xnat
 Add the tools to PATH :
export PATH=/PathToMasimatlab/trunk/xnatspiders/Xnat_tools:$PATH
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After this short course, you will be able to:
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Get our code from Masimatlab
Set up your computer (python packages, …)
Download data from XNAT using command line tools
Upload data using XNAT command tools
Dcm4chee to send big DICOM database to XNAT
Use XNAT command line tools
Project mirroring XNAT->XNAT / full
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Download from XNAT
You can download using what you learn from the
previous course :
Download file
Manage file
You can use the Xnatdownload commandline
tool developed by our lab that downloads
resources from scans or/and assessors.
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Xnatdownload
Python commandline tool developed by our lab
Present in the masimatlab svn repository:
trunk/xnatspiders/Xnat_tools/Xnatdownload
Different options to precise your download
Use: Xnatdownload -h to see the options
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XNAT view
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Upload Data to XNAT
DICOM can be uploaded using:
DicomBrowser (previous course)
dcm4che (next slides)
Xnatupload is a commandline tool developed by
our lab to upload any resources to XNAT using
three methods.
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Dcm4che (1)
Open Source clinical Image and object management
Programed in Java
Tutorial on how to upload : http://xnat.vanderbilt.edu in
Advanced resources.
Join Masimatlab on NITRC to obtain the code for
Dicom4che
 Dcmsnd present in the masimatlab/trunk/xnatspiders/dcm4che_tools/dcm4che2.0.27/bin/
 E.G: dcmsnd VandyXNAT@xnat.vanderbilt.edu:8104 /FullPathTemporatoryFolder/*
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XNAT reading DICOM
XNAT provides a DicomServer:
Remember!
Read information from the header
Add the Dicom to the PreArchive with the right
project/subject/session
XNAT uses tags from DICOM to identify where it
should be:
Usually tag (0010,4000) Patient Comments
Need to be:
“Project:ProjectIDXNAT;Subject:SubjectIDXNAT;Session:SessionIDXNAT”
E.G: Project:VUSTP;Subject:VUSTP4;Session:VUSTP4a
 Check this link to know the tags : http://mindhive.mit.edu/node/1352
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Dcm4che (2)
1. Use an IDE for java developers like Eclipse
2. Create a new project and configure the java build path
to add all the externals JARs and Class folder from
masimatlab
3. Change the SNARLdcmEdit.java file that will change
in all of your DICOM the tag of identification for
XNAT (0010,4000)
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Follow the steps in http://xnat.vanderbilt.edu “Sending
DICOM to Vanderbilt XNAT” link
4. Send the DICOMs to XNAT using dcmsnd
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dcmsnd VandyXNAT@xnat.vanderbilt.edy:8104 /path/*
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Xnatupload
Python commandline tool developed by our lab
Present in the masimatlab svn repository:
trunk/xnatspiders/Xnat_tools/Xnatupload
It can upload any resources (not only DICOM)
Three methods in the option:
Files in the same folder, using specific names
Files spread into a specific tree hierarchy
Upload only on existing
subjects/sessions/scans/assessors
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First Method of Upload
This method uploads only resources for scans.
Options : --up1
Conditions:
all the file are in the same folder
Name the files like :
 Project-x-subject-x-experiment-x-scan-x-scantype-x-series_description-xresource.extension
E.G: VUSTP-x-VUSTP5-x-VUSTP5a-x-301-x-T1-x-3W_T1-x-NIFTI.nii.gz
The project needs to exist first on XNAT
You need to select a type of session (MR/CT/PET)
Call the script :
Xnatupload -p VUSTP -d /tmp/vustp_data/ --up1 --sess MR
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Second Method of Upload
This method uploads only resources for scans.
Options : --up2
Conditions:
One Folder with a specific structure
The structure needs to be :
 Folder/subject/experiment/scan-x-scantype-x-series_description/resource/file.extension
E.G: MainFolder/VUSTP5/VUSTP5a/301-x-T1-x-3W_T1/NIFTI/file.nii.gz
The project needs to exist first on XNAT
You need to select a type of session (MR/CT/PET)
Call the script :
Xnatupload -p VUSTP -d /tmp/vustp_data/ --up2 --sess MR
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Third Method of Upload
 This method uploads only (does not create any
subject/experiment/scan or assessor on XNAT)
 Options : -o/--onlyUpload
 Conditions:
 One Folder with all the files in it (multi project)
 The files needs to have a name like :
 Project-x-subject-x-experiment-x-scan-x-resource.extension
E.G: VUSTP-x-VUSTP5-x-VUSTP5a-x-301-x-NIFTI.nii.gz
 Use the option -T to specify the kind of data (scans or assessors)
 The location needs to exist on XNAT
 Call the script :
Xnatupload -p VUSTP -d /tmp/vustp_data/ --only -T 1
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XNAT view
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XNAT command tools
 Xnatdownload and Xnatupload (already presented)
 Xnatreport
 Creates report on project(s) from XNAT
 Xnatquery
 Queries and displays XNAT at any level
 Xnatcheck
 Checks if a resource exists on specific assessors or scans
 Checks the status of assessors
 XnatSwitchProcessStatus
 Xnatsetup
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Xnatreport
Use Xnatreport -h to see the options
E.G: Xnatreport –p VUSTP
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Xnatquery
 Option
--info
for a report
Help:
Xnatquery
–hmore focus on the processes.
E.G: Xnatquery –p VUSTP --info
Xnatquery will display on the terminal all the
objects at the level you asked.
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Xnatcheck
 Xnatcheck allows you to check the existence of a resource on a
project
 Help: Xnatcheck -h
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XNAT view
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XnatSwitchProcessStatus
 The status on an assessor gives information about the job
status of this process. Our system use this status to launch
jobs.
 XnatSwitchProcessStatus allows you to change the status
of several assessors at a time.
 Help: XnatSwitchProcessStatus -h
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XNAT view
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Xnatsetup
Command tool to Setup your computer
Different setups:
Basic :
Install python packages: httplib2 / lxml / pyxnat
Set up your .bashrc or .profile
Advance:
Set up path for spiders
Redcap:
Install python packages: PyCap and Pandas
Set up your .bashrc or .profile
Some specific spiders set up to check if you have
everything to run them.
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xnat_copy
• Mirrors a Project from one XNAT instance to another
• Copies files & attributes for all Subjects/Sessions/Scans
xnat_copy [options] project
-cf
recheck existing files
-ca
recheck existing attributes
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Interactive Assignment
• Create a NITRC account and join the Masimatlab team to get
the last version of masimatlab svn repository.
• Download the code from masimatlab on NITRC
• Set up your computer (manually or with Xnatsetup):
• Download all the NIFTI from VUSTP using Xnatdownload
• Upload the VUSTP data into a new project using Xnatupload
and one of the method
• Check if a fMRIQA process in VUSTP doesn’t have a PDF
• Xnatquery --info on VUSTP
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Next time
• Create a project on REDCap and ask for API
• What is a spider:
- source code
- Which spiders already exist?
- Run spiders from your computer
• ACCRE: run spiders (status / failed / ….)
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