Difference between revisions of "Training:Workshop Prerequisite"
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| − | ='''Preparation for the Workshop''' | + | ='''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 | * 1. '''Slicer3''': software application and open-source programming environment | ||
| Line 8: | Line 8: | ||
* 4. '''Visualization Toolkit''' (VTK) environment | * 4. '''Visualization Toolkit''' (VTK) environment | ||
* 5. '''Development packages''' | * 5. '''Development packages''' | ||
| − | * 6. '' | + | * 6. '''Datasets''' |
='''Slicer3 Software''' = | ='''Slicer3 Software''' = | ||
| Line 14: | Line 14: | ||
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: | 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 | + | svn co http://www.na-mic.org/svn/Slicer3/branches/Munich2008 Slicer3 |
./Slicer3/Scripts/getbuildtest.tcl | ./Slicer3/Scripts/getbuildtest.tcl | ||
| − | ='''CMake'''= | + | Note'': Building Slicer can take up to '''2 hours'''. |
| + | |||
| + | This will install the following packages: | ||
| + | |||
| + | |||
| + | =='''CMake'''== | ||
CMake 2.6 | CMake 2.6 | ||
| − | ='''ITK environment'''= | + | |
| + | =='''ITK environment'''== | ||
ITK 3.6 | ITK 3.6 | ||
| − | ='''VTK environment'''= | + | =='''VTK environment'''== |
VTK 5.2 | VTK 5.2 | ||
='''Development packages''' = | ='''Development packages''' = | ||
| + | |||
=='''Linux'''== | =='''Linux'''== | ||
* gcc | * gcc | ||
| Line 47: | Line 54: | ||
* 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)). | * 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)). | ||
* [http://www.cygwin.com Cygwin] with the following 5 packages | * [http://www.cygwin.com Cygwin] with the following 5 packages | ||
| − | **tcltk | + | **tcltk (''Libs -> tcltk: TCL/Tk libraries'') |
| − | **svn | + | **svn (''Devel -> subversion: A version control system'') |
| − | **cvs | + | **cvs (''Devel -> cvs: Concurrent Version System'') |
| − | **unzip | + | **unzip (''Archive -> unzip: A utility for uinpacking zip files'') |
| − | **curl | + | **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). | Note: CMake and VTK will not work on a FAT formatted disk (use NTFS). | ||
| Line 62: | Line 69: | ||
* Subversion. Installation [http://downloads.open.collab.net/binaries.html 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). | * Subversion. Installation [http://downloads.open.collab.net/binaries.html 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: | |
| + | |||
| + | *[http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz ] | ||
| + | |||
| + | *[http://www.na-mic.org/Wiki/index.php/Image:AutomaticSegmentation.tar.gz AutomaticSegmentation.tar.gz] | ||
| + | |||
| + | *[http://www.na-mic.org/Wiki/index.php/Image:HelloWorld_Plugin.tar.gz HelloWorld_Plugin.tar.gz ] | ||
| + | |||
| + | *[http://www.na-mic.org/Wiki/index.php/Image:HelloWorld_Plugin.zip HelloWorld_Plugin.zip ] | ||
| + | |||
| + | |||
| + | ='''IGT Tutorials'''= | ||
| + | |||
| + | * Image Guided Therapy tutorial software and datasets: | ||
| + | ** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning IGT Workflows using Neurosurgical Planning]: Download the tutorial slides and the tutorial dataset | ||
| + | ** [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial 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 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-OpenIGTLink here] | ||
Latest revision as of 06:56, 16 June 2008
Home < Training:Workshop PrerequisiteContents
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:
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
