NCI Slicer Tutorial 03-19-2009

Course Syllabus

The National Alliance for Medical Image Computing (NA-MIC), one of the seven National Centers for Biomedical Computing (NCBC), part of the NIH Roadmap for medical research, focuses its efforts on the conversion of scientific advances from the biomedical imaging community into an open-source toolkit, so as to improve the availability and deployment of advanced software tools on a national scale. The purpose of this workshop is to provide the members of the National Cancer Institute community with a practical experience of the image processing and 3D visualization capabilities of the Slicer software platform, part of the NA-MIC toolkit.

Course Faculty

• Ron Kikinis, M.D., Professor of Radiology, Harvard Medical School

Director, Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

• Steve Pieper, Ph.D.

Isomics Inc., Cambridge MA

Logistics

• Date: Thursday March 19, 2009
• Time: 9am - 12pm
• Location: National Cancer Institutes (NCI): NCI Advanced Biomedical Computing Center, NCI-Frederick, Building 430, Ft. Detrick, Frederick, MD 21702
• Participants are required to come with their own computer (PC, Linux or MacOS).

Directions and Security

• The NCI-Frederick facility is on the base at Ft. Detrick. Coming from Washington DC, take US 15 North or Interstate 70 North and merge onto US 15 North. Take the "7th Street" exit off US 15 ; turn right at the exit; Pass the Frederick mall and the McDonalds on your right; Continue to a fork in the road, the right fork enters Ft. Detrick.
• Visitors without vehicle base passes should use the right two lanes. You will need only a picture ID, such as a drivers license. Please allow ten minutes for base entry before 9AM, as there will be a few cars in line at this time. Visitors will be asked to open the car doors and get out of the car during a routine vehicle inspection which lasts only a minute or two per car.
• Once you are passed the guard station, please turn left at the first stoplight (Porter Street) and continue a few blocks. Parking very close to building 430 is somewhat hard to find, so we suggest parking in the large parking lot on the right just before Neiman Street. Walk down Neiman street and building 430 will be across the first intersection you come to.
• The entrance to building 430 is around on the left side. There is a doorbell to ring for access to the building.

A campus map for NCI-Frederick can be found at this URL: NCI-Campus-Map

Contacts in Building 430

• If you have any trouble entering Building 430. Please call Kathy Easterday (301-846-5763), Stacy Dorsey (301-846-5761), or Curt Lisle (407-451-9386).

Agenda

• 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
• 9:10 am - 9:30 am Slicer3 Overview and Applications (Ron Kikinis)
• 9:30 am - 10:30 am Hands-on Session 1: Data Loading and 3D Visualization (Steve Pieper)
• 10:30 am - 10:45 am Coffee-break
• 10:45 am - 11:30 am Hands-on Session 2: Data Saving (Steve Pieper)
• 11:30 am - 12:00 pm Discussion and Conclusion

Preparation for the Workshop

Please complete the following items prior to the course. Support will be provided as requested

Slicer3 Software

Please install the version of Slicer3 appropriate to the platform you'll be working on during the workshop

• Windows XP: Slicer3-3.2.2008-08-20-win32.exe
• Mac OSX Darwin PPC: Slicer3-3.2.2008-08-20-darwin-ppc.tar.gz
• Mac OSX Darwin Intel: Slicer3-3.2.2008-08-20-darwin-x86.tar.gz
• Linux x86: Slicer3-3.2.2008-08-20-linux-x86.tar.gz
• Linux x86-64: Slicer3-3.2.2008-08-20-linux-x86_64.tar.gz

The instructions for installing the Slicer3 program describe the different steps of the procedure on Mac OS, Linux and Windows.

Recommended configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory.

Note: Apple Mac OS X

For Mac OS 10.4.10 (Tiger) install X11 from the OS disk 1 (not installed by default on new machines).

For Mac OS 10.5 (Leopard) visit the xquartz website and install xquartz.

Datasets

Please download the following datasets for the hands-on sessions (Linux/Mac/Windows):

• SlicerSampleVisualization-2009-02-24.zip

Back to NA-MIC Events