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XNAT and Basic K nowledge Vanderbilt University

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

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XNAT and Basic K nowledge Vanderbilt University

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  1. XNAT and Basic Knowledge Vanderbilt University

    2013-09-23 Benjamin Yvernault, Bennett Landman, Brian Boyd
  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
  3. Register and login XNAT : http://xnat.vanderbilt.edu/xnat 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.
  5. XNAT Home Screen « Other projects » : list of projects where you don’t have access. Option to request access to a project. List of your Projects Click a project to go to the project view (slide 6)
  6. Requestaccess to a Project List of projects where you don’t have access.
  7. E-mail sent to all owners XNAT email address : vuiis.cci@gmail.com An email is sent to all owners of a project when requesting access. Any owner can grant you access by clicking on the link
  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)
  9. Project View Project overview « Access » tab to manage users access for the project List of subjects Click on a subject to access the subject view (slide 8)
  10. Giveaccess to a project Tools to addusers Access levels: Collaborator Member Owner « Show List » gives the list of all XNAT users
  11. Access Levels in XNAT 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+Permissions
  13. SubjectView Click on a Session to access the session view (slide 9)
  14. Session View
  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.
  16. Scan View (1) « Show Counts » shows the resources/images rawpresents Preview of the Raw Data (DICOM/NIFTI) « Show Counts » cantake a few seconds to load
  17. Scan View (2) Preview of the Raw Data (DICOM/NIFTI)  Show Counts
  18. Processing View (1) « Show Counts » to see the resources / output PDF download link Link to the process overview (slide 13) show preview of process (snapshots) Don’t worry if it takes a while to show / pop up for the PDF and Show Counts
  19. ProcessingView (2) Seepreview Show Counts
  20. ProcessingOverview
  21. How to use XNAT Search Four ways of searching within XNAT 2) Advanced search 1) Quick search 3) Tabs (Project, Subject, …) 4) Data & Stored Searches
  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 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
  24. How to use the tabs to search? (1) You can use only one tab at a time
  25. How to use the tabs to search? (2) Search on sessions with “2” 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
  27. Create your own search (1) Use Data & Stored Searches 13253 processings
  28. Create your own search (2) Let’s search all processing that are running Filter : procstatus = Running
  29. Result of your own search (3) 13,253 Processes only 7 running
  30. Options for the search 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 Some information are missing. E.G: what is the project for each process?
  32. Save your own search 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”
  34. Download Data Downloading Data with the Action Menu on the session page : Using « Manage Files » Using « Download Images » 
  35. Download Images
  36. Manage Files Check the data to download Select the format Hit Download Click the link to download only one file
  37. WARNING 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
  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
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