Munich Workshop Agenda

This is a work in progress, agenda items subject to change.

Look at the bottom of the page for notes and updates.

Overview

XNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University in St. Louis. This two-day workshop provides:

An introduction to XNAT's functions, including new features and capabilities in the latest 1.6 release
Demonstrations of XNAT set-up, configuration, and customization
Walk-throughs of the primary tasks in XNAT, such as data uploading, image QC, and configuring projects for discrete and longitudinal studies
Advanced technical presentations for data mining, analysis, and reporting, scripting and automation, and so on
Q&A sessions with principal developers and power users of the XNAT system

All workshop attendees will receive a USB drive containing a virtual machine with XNAT 1.6 installed and configured with sample project data. If you'd like to be able to follow along with the various tutorial and practical sessions, you can bring a laptop with VMWare Player or VirtualBox installed to run the virtual machine.

Agenda

Our days will break out like this:

Thursday 9 - 10	Introduction to XNAT
	This will be a basic introduction to XNAT's capabilities and requirements, as well as some discussion about the topics that will be covered in the remainder of the workshop sessions.
Thursday 10-12	Virtual Machine Setup & Walkthrough
	This will provide some time for you to get a virtual machine installed and running. We will also perform some basic tasks: Creating a project and some subjects Configuring schema validation Uploading an image Checking validation results
Thursday 12-1	Lunch
	Lunch will be provided on-site by INCF.
Thursday 1-3	XNAT Configuration and Administration
	This session get you started working with XNAT and familiar with the most common procedures and tasks: System administration Configuration and design Managing projects and subjects User administration and project accessibility
Thursday 3-5	Pipelines, Data Transfer, and Reconstructions
	The core function of XNAT is the archiving and analysis of medical imaging data. This session will demonstrate: Setting up pipelines Uploading data (including DICOM anonymization) Creating image reconstructions Validating image sessions (XNAT2012 - Image Session Validation)
Friday 9-12	Extending and Customizing XNAT
	XNAT provides a number of different means by which you can add or tailor existing functionality to support your unique research requirements: Build folders and scripts Extending XNAT with modules from the XNAT Marketplace Creating your own modules Custom data types and user interface elements Custom REST services
Friday 12-1	Lunch
	Lunch will be provided on-site by INCF. Dan Marcus will also present the features and changes in the upcoming XNAT 2.0 release.
Friday 1-5	Open Agenda
	Possible topics include: Continued discussion of the morning's session Managing Multi-Site Studies Hackathon Q&A Collaborative projects Pyxnat Neuroimaging features

Notes, Updates and Addenda

DicomEdit

The DicomEdit documentation is not currently available on the XNAT documentation wiki, but is available on another XNAT site.

Fixing the XNAT Munich Workshop Virtual Machine

Here's how to get the DicomToNifti pipeline to work:

In the browser, log into XNAT (http://localhost:8080/xnat, admin/admin).
Click Administer->Configuration.
Click the File System tab
Change the pipeline path (at the bottom of the tab) to /opt/xnat/pipeline.
Click Save.
Open a terminal window.
Type the command:

This also fixes the issue with generating snapshot images on data archiving.