1. Deep Project Management with XNAT Vanderbilt University
Benjamin Yvernault,
Bennett Landman, Brian Boyd,

2. Requirements At this point, you should know how to :
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

3. 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 :
Set up the XNAT variables : export XNAT_USER = bob (your xnat username) export XNAT_PASS = bob (your xnat password) export XNAT_HOST =
Add the tools to PATH : export PATH=/PathToMasimatlab/trunk/xnatspiders/Xnat_tools:$PATH
Remember!
Xnatsetup

4. After this short course, you will be able to:
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

5. 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.

6. 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

7. XNAT view

8. 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.

9. Dcm4che (1) Open Source clinical Image and object management
Programed in Java
Tutorial on how to upload : in Advanced resources.
Join Masimatlab on NITRC to obtain the code for Dicom4che
Dcmsnd present in the masimatlab/trunk/xnatspiders/dcm4che_tools/dcm4che /bin/
E.G: dcmsnd /FullPathTemporatoryFolder/*

10. XNAT reading DICOM XNAT provides a DicomServer:
Remember!
XNAT provides a DicomServer:
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 :

11. Dcm4che (2) Use an IDE for java developers like Eclipse
Create a new project and configure the java build path to add all the externals JARs and Class folder from masimatlab
Change the SNARLdcmEdit.java file that will change in all of your DICOM the tag of identification for XNAT (0010,4000)
Follow the steps in “Sending DICOM to Vanderbilt XNAT” link
Send the DICOMs to XNAT using dcmsnd
dcmsnd /path/*

12. 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

13. 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-x- resource.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

14. 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

15. 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

16. XNAT view

17. 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

18. Xnatreport Use Xnatreport -h to see the options
E.G: Xnatreport –p VUSTP

19. Xnatquery Help: Xnatquery –h
Option --info for a report more focus on the processes. E.G: Xnatquery –p VUSTP --info
Help: Xnatquery –h
Xnatquery will display on the terminal all the objects at the level you asked.

20. Xnatcheck
Xnatcheck allows you to check the existence of a resource on a project
Help: Xnatcheck -h

21. XNAT view

22. 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

23. XNAT view

24. 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
Some specific spiders set up to check if you have everything to run them.

25. 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

26. 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

27. 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 / ….)