Training:Workshop Prerequisite

Preparation for the Workshop

The following components of the NA-MIC kit will be used during the workshop. Support will be provided as requested.

• 1. Slicer3: software application and open-source programming environment
• 2. CMake: cross-platform open-source build system
• 3. Insight Segmentation and Registration Toolkit (ITK) environment
• 4. Visualization Toolkit (VTK) environment
• 5. Development packages
• 6. Datasets

Slicer3 Software

Please do the following two commands to download the source code and build Slicer3 on the computer that you will be bringing to the workshop:

  svn co http://www.na-mic.org/svn/Slicer3/branches/Munich2008 Slicer3

  ./Slicer3/Scripts/getbuildtest.tcl

Note: Building Slicer can take up to 2 hours.

This will install the following packages:

CMake

CMake 2.6

ITK environment

ITK 3.6

VTK environment

VTK 5.2

Development packages

Linux

• gcc
• gcc-c++
• libX11
• libX11-devel (libX11-dev on Ubuntu)
• libXt-devel (libXt-dev on Ubuntu)
• opengl/mesa (libgl1-mesa-dev on Ubuntu)
• libncurses5-dev

Below is a Ubuntu one line install:

sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libncurses5-dev tcsh

Note: The packages names below correspond to Ubuntu 7.04. Please ensure that you use the appropriate package names for your distribution. Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command 'glxgears' runs with no errors.

Windows

• Developer Studio 8 2005 ( if installed in the default locations in "c:/Program Files" it will be detected by the build script automatically (you need to edit slicer_variables.tcl to point to the installation)).
• Cygwin with the following 5 packages
  • tcltk (Libs -> tcltk: TCL/Tk libraries)
  • svn (Devel -> subversion: A version control system)
  • cvs (Devel -> cvs: Concurrent Version System)
  • unzip (Archive -> unzip: A utility for uinpacking zip files)
  • curl (Web -> curl: Command line tool for transferring files with HTTP, HTTPS, FTP, etc.)

Note: CMake and VTK will not work on a FAT formatted disk (use NTFS).

Apple Mac OS X

For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):

• Xcode Tools (OS Disk 1, default window)
• X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See step-by-step instructions.
• X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
• Subversion. Installation options here. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).

Datasets

Please download the following datasets for the hands-on sessions:

• SlicerSampleVisualization.tar.gz

• AutomaticSegmentation.tar.gz

• HelloWorld_Plugin.tar.gz

• HelloWorld_Plugin.zip

IGT Tutorials

• Image Guided Therapy tutorial software and datasets:
  • IGT Workflows using Neurosurgical Planning: Download the tutorial slides and the tutorial dataset
  • I/O to trackers, devices, and scanners: OpenIGTLink: Install the OpenIGTLink module and the tracker simulator; download the tutorial slides, the abdominal atlas and the tool model
    • For the OpenIGTLink module, first try the precompiled binaries. Run Slicer and ensure that "OpenIGTLink" is listed in the list of modules. If OpenIGTLink does not show up, you will have to build the OpenIGTLink module from source - find the instructions here