Workshop Agenda

Breakfast & sign-in.

Coffee and pastries will be available in the lobby outside Connor Auditorium. Make sure to pick up a packet, name tag, and some schwag.

Welcome everyone! Dan will talk a bit about how the workshop is organized and give a brief update on recent XNAT developments.

We will begin the workshop by role-playing the process of gathering information at the onset of a major project. Workshop attendees will split into groups to meet with "PIs", and interview them for project requirements.

By the end of this session, users should have a good set of requirements for their new site and be able to define:

• The types of projects required
• Which data types are needed for the site
• Required imaging modalities
• Anonymization and validation requirements
• Pipeline processing

If you haven't already installed your XNAT 1.6 VM, this working lunch session is geared toward making sure you have one up and working, in preparation for the rest of the conference.

If you have already got yours installed, we recommend milling about and meeting new people.

This is a wide-ranging review of a process that is often iterative and reactive in practice, but we are condensing it down for an idealized project preparation and configuration period to hit on the main points.

• Site and Project Structure (1:40)
• Anonymization Scripts (2:20)
• Working with Visits and Protocols. Presented by Jordan Woerndle (3:00)
• Image Validation using Schematron. Presented by Mohana Ramaratnam (4:00)

Using the information we gathered in the Project Intake session, we will begin configuring our XNAT to support the BOGUS project. This includes:

• Creating and integrating modules into XNAT
• Installing custom data types - one from the XNAT Marketplace, and one provided on disk
• Enabling custom functionality and UI components

An open forum to answer questions, with a particular focus on what we've heard so far.

Feel free to post questions in advance (example: "Why does my XNAT hate me?") on this page: Attendee Questions

A working lunch lecture beginning at 12:30, featuring a discussion of working XNAT instances, including hardware requirements, server configuration, security, automation, etc.

BOGUS XNAT is ready to accept data – how will it get there? Topics include:

• The upload applet
• zip/tar.gz upload
• DICOM C-STORE
• Autoarchiving (including troubleshooting)
• The prearchive (and more troubleshooting)
• How XNAT decides where to put received data (and how to change that)
• What XNAT does to DICOM metadata (and how to change that)
• DicomEdit: XNAT's language for modifying metadata
• Getting data from remote sites, including RSNA CTP
• Using the spreadsheet uploader (Tim)

The Pipeline Engine is one of the most powerful - and mystifying - tools in the XNAT universe. Mohana, the lead architect of the Pipeline Engine, is here to teach us its secrets.

At the end of this session, attendees should be able to:

• Add pipeline to a XNAT site
• Setup an available pipeline for a project
• Guide XNAT users on launching a pipeline
• Create a new pipeline

The first 1/2 of lunch will be free, allowing people to get food, eat, talk, etc. From 12:30 to 1:30, Dan leads a talk on XNAT Roadmap, 1.6 and beyond.

Once you have data to work with, the fun begins - for your end users. This session focuses on enabling smart searches, data mining, and reporting, as well as exploring browser-based data visualization tools.

• Introduction to reports (1:30)
• Standard reports & notifications in CNDA, by Jenny Gurney (1:45)
• Building a complex report for a PI, by Jenny Gurney (2:00)
• Hands-on: Building data tables and stored searches. (2:30)
• Examples of visual data in dashboards and reports (3:00)
• Hands-on: Building a dynamic Javascript visualization from XNAT data (3:30)

Join us in Connor Auditorium for a quick introduction to the developer track followed by a 1-hour developer-focused walk-through of the XNAT Code base, with a focus on new features in XNAT 1.6.

Topics:

• How the XNAT Search Engine Works
• Codebase Overview for Developers
• How to extend the REST API

An open forum to answer questions, with a particular focus on puzzling aspects of XNAT code or functionality.

Feel free to post questions in advance (example: "Why does my XNAT hate me?") on this page: Attendee Questions