Difference between revisions of "Training:RobartsResearchInstitute2008 Workshop Prerequisite"

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='''Preparation for the Workshop - Programmers'''=
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='''To Do Before the Workshop'''=
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* '''Install Slicer from the source code''' (downloading a binary is not enough)
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* '''Install the additional software'''
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* '''Download the datasets'''
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='''Preparation for the Workshop'''=
  
 
The following components of the NA-MIC kit will be used during the workshop.  
 
The following components of the NA-MIC kit will be used during the workshop.  
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<span style="background-color: yellow"> Note'': Building Slicer can take up to '''2 hours'''.</span><br />
 
<span style="background-color: yellow"> Note'': Building Slicer can take up to '''2 hours'''.</span><br />
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 +
<span style="background-color: yellow"> Note'': the VTK, ITK, and KWWidgets cvs servers have been heavily loaded.  If your build fails, you should re-run the getbuildtest script to be sure all the libraries have properly built.</span><br />
 +
 +
Also note that some of the tests may fail due to warnings - don't worry about this.  As long as the slicer user interface built on your machine comes up on you will be ready for the workshop.
  
 
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.
 
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.
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== '''Windows''' ==
 
== '''Windows''' ==
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* 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)).
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* 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 (''Libs -> tcltk: TCL/Tk libraries'')
 
**tcltk (''Libs -> tcltk: TCL/Tk libraries'')
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**curl (''Web -> curl: Command line tool for transferring files with HTTP, HTTPS, FTP, etc.'')
 
**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).
 +
* If you do not have Developer Studio 8 2005, follow the instructions on [https://www.slicer.org/wiki/Slicer3:Build_Instructions_Windows this page].  However, run:
 +
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  svn co http://svn.slicer.org/Slicer3/branches/Stanford2008 Slicer3
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 +
instead of
 +
 +
  svn co http://svn.slicer.org/Slicer3/trunk Slicer3
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You will need to manually install a newer version of cmake as part of the process described in the link.
  
 
== '''Apple Mac OS X''' ==
 
== '''Apple Mac OS X''' ==
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* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
 
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
 
* 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).
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='''Additional software'''=
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* Follow [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial#Step_2:_Install_the_OpenIGTLink_module the instructions to install the OpenIGTLink loadable module].
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** '''If you downloaded the precompiled version (binary):'''
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** Check to make sure that OpenIGTLink appears as a module in Slicer's list of modules (run Slicer, open the modules list by clicking on "Data", and ensure that OpenIGTLink is in the list).
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** If OpenIGTLink does not appear, then you must build the OpenIGTLink module from source.
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* Follow [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial#Step_3:_Install_the_tracker_simulator the instructions to install the tracker simulator].
  
 
='''Datasets'''=
 
='''Datasets'''=
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*[http://www.na-mic.org/Wiki/index.php/Image:HelloWorld_Plugin.zip HelloWorld_Plugin.zip ]
 
*[http://www.na-mic.org/Wiki/index.php/Image:HelloWorld_Plugin.zip HelloWorld_Plugin.zip ]
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*[[Media:MRGuidedProstateInterventions.zip | MRGuidedProstateInterventions.zip]]
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*[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=4171 Abdominal_Atlas_2008.zip]
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*[http://wiki.na-mic.org/Wiki/images/b/b2/Tool.vtk Tool.vtk]
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**If Windows saves the file as Tool.htm instead of Tool.vtk:
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**Select Start->Run
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**type "cmd"
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**type "cd <directory where Tool.htm is>"
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**type "move Tool.htm Tool.vtk"
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*[[Media:NeurosurgicalPlanning_all.tar.gz | NeurosurgicalPlanning_all.tar.gz]]
  
  
−
[http://www.na-mic.org/Wiki/index.php/Robarts_Training_Session Back to Robarts Research Institue 2008 Slicer Workshop]
+
[http://www.na-mic.org/Wiki/index.php/Robarts_Training_Session Back to Robarts Research Institute 2008 Slicer Workshop]

Latest revision as of 18:07, 10 July 2017

Home < Training:RobartsResearchInstitute2008 Workshop Prerequisite

To Do Before the Workshop

  • Install Slicer from the source code (downloading a binary is not enough)
  • Install the additional software
  • Download the datasets

Preparation for the Workshop

The following components of the NA-MIC kit will be used during the workshop.

  • 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://svn.slicer.org/Slicer3/branches/Stanford2008 Slicer3

  ./Slicer3/Scripts/getbuildtest.tcl

Note: Building Slicer can take up to 2 hours.

Note: the VTK, ITK, and KWWidgets cvs servers have been heavily loaded. If your build fails, you should re-run the getbuildtest script to be sure all the libraries have properly built.

Also note that some of the tests may fail due to warnings - don't worry about this. As long as the slicer user interface built on your machine comes up on you will be ready for the workshop.

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.

This will install the following packages:

  • CMake 2.6
  • ITK 3.8
  • 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).

  • If you do not have Developer Studio 8 2005, follow the instructions on this page. However, run:
  svn co http://svn.slicer.org/Slicer3/branches/Stanford2008 Slicer3

instead of 

  svn co http://svn.slicer.org/Slicer3/trunk Slicer3

You will need to manually install a newer version of cmake as part of the process described in the link.

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).

Additional software

Datasets

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

  • Tool.vtk
    • If Windows saves the file as Tool.htm instead of Tool.vtk:
    • Select Start->Run
    • type "cmd"
    • type "cd <directory where Tool.htm is>"
    • type "move Tool.htm Tool.vtk"


Back to Robarts Research Institute 2008 Slicer Workshop

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