User:Mseeland

Wiki of Madeleine Seeland

General Information

About myself

I am a grad student of Management Information Systems at the University of Mannheim, Germany. I'm involved in the Diffusion Tensor Imaging (DTI) project in the Laboratory of Mathematics in Imaging. Currently I'm working on two-tensor tractograohy for Neurosurgery. I will document my research experience as a diploma thesis, which I need for completing my studies in Germany.

Contact information

E-mail: mseeland (at sign) bwh.harvard.edu

Collaborators & Contacts

• Supervisors: C-F Westin, Nobuhiko Hata
• Gordon Kindlmann
• Sharon Peled
• Alireza Radmanesh
• regarding Python: Demian Wassermann, Steve Pieper, Sylvain Bouix, Julien de Siebenthal

Project: Two-Tensor Tractography integration into Slicer

• Integration of two-tensor tractography into Slicer using Python
• My part: Interface between Python and Slicer
• The Teem Python API will be provided by Gordon Kindlmann

How to enable Python in Slicer 3.3

• The current version of Slicer, Slicer 3.2, does not support Python. To use Python you need to install Slicer 3.3.

To build Slicer Version 3.3, just do the following two commands:

 svn co http://svn.slicer.org/Slicer3/trunk Slicer3
 ./Slicer3/Scripts/getbuildtest.tcl

• In Slicer 3.3, Python support is disabled by default. In order to enable Python, just follow the next steps:

1. Edit slicer_variables.tcl
   1. Change "set ::USE_PYTHON "off"" to "on"
2. Optional: If you prefer to use your system Python installation, see here: [1]
3. Optional: installing SciPy, see here: [2]

Rebuild Slicer3 using "getbuildtest.tcl":

./Slicer3/Scripts/getbuildtest.tcl

A new menu command Python Interpreter should appear on the Window menu in Slicer. This command should bring up the Python Console window.

Status/Progress

• Trying to enable Python in Slicer -> done
• Python tutorials
• get familiar with the existing Slicer3 tractography module
• implement the seeding part of the existing Slicer3 tractography module's functionality in Python

Information

• Diffusion Tensor Analysis in Slicer: http://www.na-mic.org/Wiki/images/0/04/Slicer3diffusionTutorial7.pdf
• Building a Slicer 3 Module GUI: http://www.slicer.org/pages/Building_a_Slicer_3_Module_GUI

Python:

• SlicerWiki about Python: http://www.slicer.org/slicerWiki/index.php/Slicer3::Python
• Python example modules in Slicer: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Python