1. XNAT and Basic Knowledge Vanderbilt University 2013-09-23 Benjamin Yvernault, Bennett Landman, Brian Boyd 1

2. After this short course, you will be able to: –Register and Log in to XNAT –See your projects and join other projects –Manage access permissions –Browse data and view image previews –Search for projects/subjects/sessions and corresponding data –Download images and stored meta-data 2

3. Register and login XNAT : http://xnat.vanderbilt.edu/xnat 3  Register by clicking the link and completing the form.  Enter username and password if you already have an account

4. PI Account Info  XNAT account for PI with an IRB approval are automatically created  Username : firstnamelastname  Password : random password  Click “Forgot password or username” to retrieve your username and reset your password for the first connection. 4

5. XNAT Home Screen 5  Click a project to go to the project view (slide 6) « Other projects » : list of projects where you don’t have access. Option to request access to a project. List of your Projects

6. Request access to a Project 6 List of projects where you don’t have access.

7. E-mail sent to all owners 7  An email is sent to all owners of a project when requesting access.  Any owner can grant you access by clicking on the link  XNAT email address : vuiis.cci@gmail.com

8. XNAT Data Hierarchy Project –Subject Experiment / Session –Scan »Resources : Raw Image Data (various formats, thumbnail snapshots, log files) –Assessor / Processing »Resources : processed Data (output images/files, PBS scripts, outlog files, text files) 8

9. Project View 9  Click on a subject to access the subject view (slide 8) List of subjects Project overview « Access » tab to manage users access for the project

10. Give access to a project 10 Tools to add users Access levels: Collaborator Member Owner « Show List » gives the list of all XNAT users

11. Access Levels in XNAT 11  Data relationship between projects :  Shared (read-only) : Data shared from another project can be deleted. You need access to the primary project.  Owned (All access) : Data owned by the project. Access depends on the user access.  User Access :  Collaborator : users with read-only access  E.G : Consultant, people off site …  Member : users with management permissions on the data that the project owns. WARNING: no access to the prearchive  E.G : Image Analyst…  Owner : users with all permissions on the data owned by the project and the project itself  E.G: PI, Engineers, developers, script runners, Image Analyst, etc…

12. User Roles and Permissions  More information at :https://wiki.xnat.org/display/XNAT16/User+Roles+and+Permiss ionshttps://wiki.xnat.org/display/XNAT16/User+Roles+and+Permiss ions 12

13. Subject View 13  Click on a Session to access the session view (slide 9)

14. Session View 14

15. What’s the difference between scans and processes?  Scan : raw data coming from a scanner with different transcodings/formats (e.g. T1 with DICOM, NIFTI and PAR/REC format)  Processing (or Assessor in XNAT vocabulary) : processed Data. All files produced by a script using data from one scan / multiple scans / another Processing data. 15

16. Scan View (1) 16  « Show Counts » can take a few seconds to load « Show Counts » shows the resources/images raw presents Preview of the Raw Data (DICOM/NIFTI)

17. Scan View (2) 17  Preview of the Raw Data (DICOM/NIFTI)  Show Counts

18. Processing View (1) 18 « Show Counts » to see the resources / output Link to the process overview (slide 13) PDF download link show preview of process (snapshots)  Don’t worry if it takes a while to show / pop up for the PDF and Show Counts

19. Processing View (2) 19  See preview  Show Counts

20. Processing Overview 20

21. How to use XNAT Search 21  Four ways of searching within XNAT 1) Quick search 2) Advanced search 4) Data & Stored Searches 3) Tabs (Project, Subject, …)

22. How to use “quick search”?  Type a label that you want to search/access  e.g. search “208404”  Useful when you know what you are looking for  E.G : I am looking for the subject 208404  Only works if the label exists in the database 22 Results: Two projects  one subject  one experiment Link to access data

23. How to use “advanced search”?  Advanced search is difficult to understand  Avoid using it unless you really want to understand how it works (slide 26 for more details)  Link to the XNAT wiki :  https://wiki.xnat.org/display/XNAT16/Using+Advanced+Search https://wiki.xnat.org/display/XNAT16/Using+Advanced+Search 23

24. How to use the tabs to search? (1) 24  You can use only one tab at a time

25. How to use the tabs to search? (2)  Search on sessions with “2” 25 Why? Filters

26. Warning with search :  XNAT identifies a Session / Subject / Process by a Label or a ID (both unique, Scan ID and label are the same)  XNAT IDs are automatically generated  XNAT searches both Label and ID  Advanced Search will check only the ID and most of the time you don’t know the ID but the Label 26

27. Create your own search (1)  Use Data & Stored Searches 27 13253 processings

28. Create your own search (2) 28  Let’s search all processing that are running  Filter : procstatus = Running

29. Result of your own search (3) 29  13,253 Processes only 7 running

30. Options for the search 30  Spreadsheet will download the content of the tab as a.csv file  Email will send a link to the search  Save (x2) will be explain next slide  Show XML displays the spreadsheet data in XML format  You can “Add columns” to your spreadsheet  Join to … will give you the possibility to add an other type of search

31. Add columns 31  Some information are missing. E.G: what is the project for each process?

32. Save your own search 32  Using the options save search will open a pop-window  You should use “Save New Search” when you are using a previous search that you don’t want to delete

33. Reopen your search : “Stored search” 33

34. Download Data 34 Downloading Data with the Action Menu on the session page :  Using « Manage Files »  Using « Download Images »

35. Download Images 35

36. Manage Files 36 1.Check the data to download 2.Select the format 3.Hit Download Click the link to download only one file

37. WARNING 37  The scissors will delete the resources/images/output files. Use with caution

38. Interactive Assignment Create an account or login to your account Log in as “vuiistest” password “password” and grant yourself ‘MEMBER’ access to the project VUSTP. Count the number of scans in the project Count the number of sessions in the project Find an MPRAGE scan Create a stored search for MPRAGE scans Download an MPRAGE image 38

39. Next time 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 39