Dissemination:Workshop Feb17

Workshop Information:

• Location: UCSD BIRN-CC
• List of Participants
• Logistics
• Attendee Feedback

Goals of workshop

• To provide hands-on development training in ITK and Slicer to NAMIC participants and their collaborators
• To establish contact between ITK and Slicer experts and the group of students and developers of the NAMIC community.
• To obtain feedback on how ITK and Slicer satisfy the needs of the algorithms that are being developed in NAMIC

Preparation for Workshop -- Important Information for all attendees

All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.

• Ensure that you are on the mailing list namic-dissemination. If you are not planning on attending the workshop and are on the mailing list, please unsubscribe yourself.
• Complete the background questionaire.
• Please install ITK, VTK, and Slicer as soon as possible, preferably on a machine that you will be bringing to the workshop, and definitely before the course.
  • Slicer
    • Build a Development installation of Slicer (includes CMake, ITK, VTK, Tcl Wrapping, and Slicer source code) Slicer:Slicer2.4_Building
    • Using your newly built Slicer, download data and look at the online tutorial Slicer:Slicer2.4_Getting_Started.
  • ITK Examples
    • After installing Slicer, download Tar.gz of ITK examples that will be used in the workshop.
    • As part of the Slicer installation, you will have built copies of CMake, VTK, and ITK needed for the exercises, but you will need to configure access to these libaries for running the exercises.
      • For Linux, assuming you put your slicer2 checkout in your home directory:
        • add the following to your PATH: ~/slicer2/Lib/linux-x86/CMake-build/bin
        • add the following to your LD_LIBRARY_PATH: ~/slicer2/Lib/linux-x86/Insight-build/bin:~/slicer2/Lib/linux-x86/VTK-build/bin
      • For Windows, assuming you put your slicer2 checkout in c:/slicer2, add the following directories to your system Path environment variable: c:\slicer2\Lib\win32\CMake-build\bin;c:\slicer2\Lib\win32\Insight-build\bin\release;c:\slicer2\Lib\win32\VTK-build\bin\release
      • Information on setting Windows environment variables is available here.
    • Learning about ITK with the online ITK Tutorial Getting Started I. This tutorial includes how to download, configure and install ITK, as well as how to run the first minimal examples. The basic ITK installation was done automatically as part of the Slicer installation, but this tutorial will provide you the background on CMake needed to build the exercises for the workshop.

If you would like to try a 1-click (maybe 1.5 click) process using Pipeline to install ITK, VTK, and the exercises above, please go to InstallationPipelines.

We will be happy to assist anybody who may encounter difficulties in the process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by Luis Ibanez, Steve Pieper and other experts in ITK and Slicer. If everyone has completes these tutorials successfully we will be able to focus on how to focus on showing you how to create applications with ITK and Slicer during the workshop.

Agenda

Day 1--Slicer

• 9-9:30am:Welcome and Objectives(Ron Kikinis, Tina Kapur)
• 9:30-10:15am: NA-MIC Software Engineering Methodology and Resources (Dan Blezek)
• 10:15-10:30 Break
• 10:30-11:15am Developers tools (Steve Pieper)
• 11:15-12noon: Slicer Overview, Slicer Demo, Slicer Build and Deploy System (Steve Pieper)
• noon-1pm: lunch
• Get Data: http://slicerl.bwh.harvard.edu/tmp/dtiviz.tar.gz

• 1-1:30pm: DTI Processing Demo (Raul San Jose)
• 1:30-2:30 Slicer Architecture, and Compiling Custom Modules (Steve Pieper)
• 2:45-3:00 Break
• 3:00-3:45pm: Integrating ITK/VTK modules in Slicer Slicer and ITK I/O factory generic readers module (Raul San Jose)
• 3:45 - 4:30 ITK/Slicer Integration Exercises. Download exercise material
• 4:30-5pm: Introduction to the UCSD Data Grid Infrastructure (Mark James, Jason Gerk)
• 5-5:15pm: wrap-up (Tina Kapur)

Day 2--ITK

• 9:00am-noon: ITK Architecture (Luis Ibanez)
• noon-12:30: lunch
• 12:30-1:30pm: ITK Filtering (Luis Ibanez)
• 1:45-3pm: ITK Segmentation (Luis Ibanez, Josh Cates)
• 3-3:20pm: break
• 3:20-4:50pm: ITK Image Registration (Luis Ibanez)
• 5pm-6pm: Intro to VTK & Combining ITK and VTK (Luis Ibanez)
• 6pm: Wrap-up (Tina Kapur)