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XNAT and Basic Knowledge Vanderbilt University

2013-09-23

Benjamin Yvernault,

Bennett Landman, Brian Boyd

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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

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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

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PI Account Info

XNAT account for PI with an IRB approval are automatically createdUsername : firstnamelastnamePassword : random password

Click “Forgot password or username” to retrieve your username and reset your password for the first connection.

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XNAT Home Screen

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

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Request access to a Project

List of projects where you don’t have access.

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E-mail sent to all owners

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

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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)

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Project View

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

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Give access to a project

Tools to add users

Access levels:• Collaborator• Member• Owner

« Show List » gives the list of all XNAT users

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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 prearchiveE.G : Image Analyst…

Owner : users with all permissions on the data owned by the project and the project itselfE.G: PI, Engineers, developers, script runners, Image Analyst, etc…

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User Roles and Permissions

More information at :https://wiki.xnat.org/display/XNAT16/User+Roles+and+Permissions

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Subject View

Click on a Session to access the session view (slide 9)

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Session View

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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.

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Scan View (1)

« Show Counts » can take a few seconds to load

« Show Counts » shows the resources/images raw presents

Preview of the Raw Data (DICOM/NIFTI)

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Scan View (2)

Preview of the Raw Data (DICOM/NIFTI)

 Show Counts 

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Processing View (1)« 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

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Processing View (2)

See preview

Show Counts

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Processing Overview

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How to use XNAT Search

Four ways of searching within XNAT

1) Quick search

2) Advanced search

4) Data & Stored Searches3) Tabs (Project, Subject, …)

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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 forE.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

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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

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How to use the tabs to search? (1)

You can use only one tab at a time

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How to use the tabs to search? (2)

Search on sessions with “2”

Why?

Filters

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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 generatedXNAT searches both Label and IDAdvanced Search will check only the ID and

most of the time you don’t know the ID but the Label

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Create your own search (1)

Use Data & Stored Searches

13253 processings

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Create your own search (2)

Let’s search all processing that are running Filter : procstatus = Running

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Result of your own search (3)

13,253 Processes only 7 running

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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

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

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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

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Reopen your search : “Stored search”

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Download Data

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

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Download Images

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Manage Files

1. Check the data to download

2. Select the format3. Hit Download

Click the link to download only one file

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

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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

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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