ShortCourse2 - vuiis xnat

Report
XNAT and Advanced Knowledge
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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–
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Register and Log in to XNAT
See your projects and join projects
Manage access permissions
Browse data and view image previews
Search for projects, subjects, and data
Download imaging data, processed, and stored metadata
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After this short course, you will be able to:
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Create project / sharing data
Delete scans / sessions / projects
Use the Pre-Archive
Upload scans through DicomBrowser
Quality Assurance
– Mark scans as usable / questionable / etc.
– Mark processing status
– View QA results in RedCAP
• Use Basic XNAT tools on ACCRE
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Creating a project / sharing Data
 You can create new projects on XNAT if you want to
store sessions in a different project than your PI project.
 You can also share the data from the PI project to your
project. The processed results and transcodings will be
created in your project and not in the main project.
 Rules about the project abbreviation:
1) Don’t use only the PI name for a project name (it already
exists)
2) Only one word, you can use ‘_’. No spaces.
3) Use PI_project . E.G : ZALD_TTS
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Create a project
Project Accessibility:
 Protected: Any users can see the project but not access it or
the data. (Use this one by default)
 Private: Nobody can see the project except the members
 Public: Project accessible by all users
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Sharing Data
 You can not share a project, a scan or an assessor to an other project
 You can only share a full subject or a full experiment
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Why sharing Data?
All scans coming from VUIIS scanners are
automatically added to the Pre-Archive under the
PI name.
PI projects are automatically created on XNAT.
All scans for a PI should be archive into the PI
name project but one PI can have several projects
Sharing the data allows you to use the data into
different projects and organize your sessions.
E.G: ZALD project is sharing data with ZALD_TTS and ZALD_TTS_PILOT
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Delete
A lot of different ways to delete scans, assessors,
sessions, subjects, or Projects on XNAT
You need to be an owner to delete Data
If a project has Data shared from an other project,
you need to be an owner of the main project (the
one sharing the data)
Be careful when deleting, it’s permanent.
It might take some time to delete. Be patient.
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Delete Project
 From “delete” link in
project, you can manage
what you want to delete
in the whole project.
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Delete Subject
 You can not delete a subject with this link when you
have processes in the sessions
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Delete Sessions
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Delete Assessors
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Delete Resources / Files
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VUIIS scans
For VUIIS : Scans are automatically sent to the prearchive with the project name equal to the PI name.
 E.G : LANDMAN
This project name can be changed using an option in
the pre-archive (slide 16)
What happens if there is an error? How do you fix it?
What about scans outside VUIIS?
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Pre-Archive
 One Session Actions
 Filter/se
arch
 Multi-session Actions
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Different Actions
ARCHIVE: transfer the session(s) chosen from the
prearchive into the archive
CHANGE PROJECTS: Change the project on the
session
DELETE: Delete the session from the prearchive
RESET : Check if there are files missing. If you see
any files missing, you should use RESET. If they
don’t appear after RESET, you might need to
request to resent the session(s) to XNAT.
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Pre-Archive : One session at a time
 Archive only one session allows you to check the scans in the
sessions
XNAT will not
archive the session if
a scan doesn’t have a
type. Set it with a
space to set it to
nothing.
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Pre-Archive several sessions
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Errors in the session
 Common errors:
 Session already exists -> ERROR status
 Scans missing in a session
 Session set to ERROR (error during the process of sending the data to
XNAT)
 Reset (action to reset the scans on XNAT) can fix the two last
errors.
 Send an email to the administrator to request session be resent
 Step 1 : Delete the sessions (WARNING: Sending the session again
will fail if the session is still in the prearchive)
 Step 2 : Ask administrator [email protected] to send again
the session to pre-archive
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Outside VUIIS
Scans from VUIIS are automatically sent to the
Pre-Archive.
What about scans, sessions, or DICOMs coming
from outside the VUIIS scanner?
XNAT can receive scans from different sources.
XNAT provides a DICOM server.
You can send scans (DICOM) to XNAT using
specific tools (DicomBrowser, dcm4che …)
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No Protected Health Information
into XNAT
18 HIPAA (Health Insurance Portability and Accountability Act) identifiers
to avoid putting into XNAT: http://cphs.berkeley.edu/hipaa/hipaa18.html
1. Names
10. Account numbers
2. All geographical subdivisions smaller than a State
11. Certificate/license numbers
3. All elements of dates (except year)
12. Vehicle identifiers and serial numbers, including license
plate numbers
4. Phone numbers
13. Device identifiers and serial numbers
5. Fax numbers
14. Web Universal Resource Locators (URLs)
6. Electronic mail addresses
15. Internet Protocol (IP) address numbers
7. Social Security numbers
16. Biometric identifiers, including finger and voice prints
8. Medical record numbers
17. Full face photographic images and any comparable
image
9. Health plan beneficiary numbers
18. Any other unique identifying number, characteristic, or
code (note this does not mean the unique code assigned by
investigator to code the data)
the
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XNAT and DICOM
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: http://mindhive.mit.edu/node/1352
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Change the Tag in DICOM
 To modify DICOM header (remove PHI for example), you can use
DicomBrowser (http://nrg.wustl.edu/software/dicom-browser/ )
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Sending DICOM to XNAT




Host: xnat.vanderbilt.edu
Port: 8104
Remote AE title: VandyXNAT
Local AE title: VandyXNAT
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Quality Assurance (1)
 Using XNAT and RedCap
 All assessors have a status. Standard job Status :

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





NEED_INPUTS
NEED_TO_RUN
JOB_RUNNING
JOB_FAILED
READY_TO_UPLOAD
UPLOADING
READY_TO_COMPLETE
COMPLETE
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Quality Assurance (2)
 All assessors have also a QA status. Standard QA Status :
 Job Pending
 Failed
 Passed
 Needs QA
 RERUN
 When an assessor has a job status set to COMPLETE, you
can check the QA and set the QA status of the assessor to
the value that fit you.
 RERUN means that the script that launch jobs will rerun
your QA process on this assessor.
 Sync the status between XNAT and REDCap
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Check QA on XNAT
 Click on + to see the preview
 Click the link to download the pdf
 Click on it to see it on a new page
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Edit Scan Usability
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Edit Assessors Status on XNAT
 Click on Edit
 Change the variables
you want to edit.
 Click to access the
 Change theassessor
QA status
that you
to Failed orwant
Passed
or
to edit
an other status that fit
your analysis.
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REDcap
REDCap is a secure, web-based application for
building and managing online surveys and
databases.
Why REDCap?
You can store Protected Health Information (PHI) in
REDCap. NEVER STORE ANY PHI INTO XNAT.
Right now, four QA scripts send data from
XNAT to REDCap keeping the same labels:
fMRIQA, VBMQA, DTIQA and FreeSurfer
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Check QA on REDCap (1)
 Redcap : https://redcap.vanderbilt.edu
 Home page
with all your
projects
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Check QA on REDCap (2)
1)
2)
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Check Records with Record Status
Dashboard
Using REDcap, you can access Record and check
the stats. If the libraries have a lot of data, it will
be slow, so be patient.
 Record Status Dashboard
 Add/Edit Records
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Record Status Dashboard
 Different libraries
(instruments in REDcap
vocabulary)
 Record with quality
Green shows where
there are data.
 Yellow tag for quality status.
By default, yellow to unverified.
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Add/Edit Records
 Select complete
or incomplete
record
 Click on the
instruments
you need
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Change status on REDcap
At the bottom of the Main Instrument record,
there is a box to change the status of a record to
complete /Incomplete / Unverified (default value)
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Data Export Tool
Faster way to check big data instruments
Be patient when exporting the Data (several
minutes for big project)
 You can open the csv file with Excel
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Basic XNAT Tools
Masimatlab NITRC repository has different
useful XNAT command tools :





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Xnatreport
Xnatquery
Xnatdownload
Xnatupload
Xnatcheck
XnatSwitchProcessStatus
Check the
masimatlab/trunk/xnatspiders/Xnat_tools
folder or on the wiki (link below).
Tutorial on http://xnat.vanderbilt.edu
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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 :
 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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Interactive Assignment
• Join the project “VUSTP”
• Download from subject VUSTP4 session VUSTP4a scan 1 the DICOM
• Create a new project
• Download DicomBrowser : http://nrg.wustl.edu/software/dicom-browser/
• Change the header with DicomBrowser to match your new project, gives a
subject and session name
• Send the DICOM to XNAT using DicomBrowser
• Check the Pre-Archive
• Archive the session
• Delete the project
• Go on Redcap and look at VUSTP project using the account
– Username: vuiisdem
– Password: seminar_demo1
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Next time
• Upload / download data from XNAT
using command tools
• Dcm4chee to send DICOM backend
• Use XNAT tools
• Project miroring XNAT->XNAT / full
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