TubeTK/Slicer: Difference between revisions

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__NOTITLE__
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'''[[TubeTK|Home]]'''
*[[TubeTK/About|About]]
*[[TubeTK/Images|Image Gallery]]
*[[TubeTK/Data|Data and Publications]]
<br>
----
<br>
'''For Users'''
* [[TubeTK/Installation|Installation]]
* [[TubeTK/Documentation|Methods & Apps]]
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]
* [[TubeTK/OsiriX|TubeTK with OsiriX]]
<br>
----
<br>
'''For Developers'''
* [[TubeTK/Development|Development Docs]]
<br>
----
<br>
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''
<br>
<br>
----
<br>
'''[[TubeTK/Contact|Contact Us]]'''
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= TubeTK in 3D Slicer =
= TubeTK in 3D Slicer =


* '''Note that these instructions are under development'''
== Overview ==
* Please use [http://www.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]
 
* Note that there are different instructions for '''users''' and '''developers'''
Slicer 3D is the recommended platform for using TubeTK. Using TubeTK stand-alone from the command-line is also well supported.
 
You must first install Slicer, and then build TubeTK using that installed version of Slicer to provide the dependencies for TubeTK (e.g., ITK, VTK, CTK).


== Users ==
== Details ==


=== Download 3D Slicer ===
=== Get CMake ===
* Download from http://www.slicer.org/pages/Special:SlicerDownloads
* Select "Type of Download": Snapshots
* Choose your operating system: Windows, Mac OS X, Linux or Solaris
* File to download: Slicer3-4.0.alpha


=== Add TubeTK's Command Line Modules ===
Install the current stable release of CMake
* Copy all of the TubeTK plugins to Slicer's plugins directory:
* Download binaries from http://www.cmake.org
cp '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/* '''<YourSlicerDirectory>'''/lib/Slicer3/Plugins


=== Run 3D Slicer ===
=== Get 3D Slicer ===
cd '''<YourSlicerDirectory>'''
Install the current stable release of Slicer
./Slicer3
* '''Download 3D Slicer Binaries:''' from http://download.slicer.org/
* '''Or, build 3D Slicer from source:''' [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/Build_Instructions Slicer4 Build Instructions]
** Configuration recommendations:
*** In CMake, turn-on advanced options and change BUILD_TYPE to Release
*** In CMake, change Slicer_USE_PYTHONQT_WITH_TCL to OFF


* The TubeTK modules will now be in the list of modules
=== Get Boost (optional) ===
Boost is used by select TubeTK applications.
* Boost must be built from source to resolve linking errors on 64 bit machines on current binaries for Boost
* Version 1.54 or later is needed
* Download from http://www.boost.org/


== Developers ==
=== Build TubeTK using Slicer ===
TubeTK will use Slicer's ITK, VTK, and other libraries during its build process, to ensure compatibility with Slicer.
* In CMake, set the following options
** BUILD_TYPE = Release
** USE_SLICER_MODULES = True


=== Build 3D Slicer ===
=== Configure Slicer to load TubeTK's modules ===
* Build Slicer4 according to the [http://www.slicer.org/slicerWiki/index.php/Slicer4_Build_instructions Slicer4 Build Instructions]
Run Slicer
* Edit -> Application Settings -> Modules -> Additional module paths (click >> to the right of the box, then the Add button)
* Select '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/
* Restart Slicer


=== Add TubeTK's Command Line Modules ===
=== Restart 3D Slicer ===
* Copy all of the TubeTK plugins to Slicer's plugins directory:
* On restart, the TubeTK modules will now be in the list of modules. All TubeTK module names end with (TubeTK)
mkdir '''<YourSlicerDirectory>'''/Slicer-build/lib/Slicer3/Plugins/TubeTK
  cp '''<YourTubeTKBuildDirectory>'''/TubeTK-Build/lib/TubeTK/Plugins/* '''<YourSlicerDirectory>'''/Slicer-build/lib/Slicer3/Plugins/TubeTK


=== Run 3D Slicer ===
|}
cd '''<YourSlicerBuildDirectory>'''/Slicer-build
./Slicer


* The TubeTK modules will now be in the list of modules
[[Category:TubeTK|Slicer]]

Latest revision as of 14:20, 6 January 2015

__NOTITLE__


TubeTK Header.jpg

Home




For Users




For Developers




Report Bugs
Request Features




Contact Us

TubeTK in 3D Slicer

Overview

Slicer 3D is the recommended platform for using TubeTK. Using TubeTK stand-alone from the command-line is also well supported.

You must first install Slicer, and then build TubeTK using that installed version of Slicer to provide the dependencies for TubeTK (e.g., ITK, VTK, CTK).

Details

Get CMake

Install the current stable release of CMake

Get 3D Slicer

Install the current stable release of Slicer

  • Download 3D Slicer Binaries: from http://download.slicer.org/
  • Or, build 3D Slicer from source: Slicer4 Build Instructions
    • Configuration recommendations:
      • In CMake, turn-on advanced options and change BUILD_TYPE to Release
      • In CMake, change Slicer_USE_PYTHONQT_WITH_TCL to OFF

Get Boost (optional)

Boost is used by select TubeTK applications.

  • Boost must be built from source to resolve linking errors on 64 bit machines on current binaries for Boost
  • Version 1.54 or later is needed
  • Download from http://www.boost.org/

Build TubeTK using Slicer

TubeTK will use Slicer's ITK, VTK, and other libraries during its build process, to ensure compatibility with Slicer.

  • In CMake, set the following options
    • BUILD_TYPE = Release
    • USE_SLICER_MODULES = True

Configure Slicer to load TubeTK's modules

Run Slicer

  • Edit -> Application Settings -> Modules -> Additional module paths (click >> to the right of the box, then the Add button)
  • Select <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins/
  • Restart Slicer

Restart 3D Slicer

  • On restart, the TubeTK modules will now be in the list of modules. All TubeTK module names end with (TubeTK)