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

Project Description

• 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. In order 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]. However, there are still problems adding scipy in Slicer, whcih are not fixed yet.

• 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.

Teem Python wrapping

• The python wrappings are based on ctypes, as well as a ctypes code generator (called "ctypeslib")
  • http://python.net/crew/theller/ctypes
  • http://starship.python.net/crew/theller/wiki/CodeGenerator
  • http://starship.python.net/crew/theller/ctypes/old/codegen.html
• Ctypes is a standard part of python, by which C functions in a shared library can be called from Python

• How to create Python wrappings for Teem:

• GETTING THE SOFTWARE
  • Python 2.6 can be got here (anything after 2.5 should work): http://www.python.org/download/
  • get gccxml version 0.9.0, which can be got by CVS as described here: http://www.gccxml.org/HTML/Download.html
    • follow the installation as described here: http://www.gccxml.org/HTML/Install.html
  • use a version of ctypeslib which work with the version of gccxml:

 * http://svn.python.org/projects/ctypes/branches/ctypeslib-gccxml-0.9

• • But this requires some patches to work; the content of the "fixes.patch file can be found here: [[3]]:

  svn co http://svn.python.org/projects/ctypes/branches/ctypeslib-gccxml-0.9
  cd ctypeslib-gccxml-0.9
  patch -p0 < ../fixes.patch
  cd ..

• • ctypeslib is written in python => there's nothing new to compile at this point

Status/Progress

Month	Week #	Start Date - End Date	Done	Date Done
	Try to compile teem with levmar (= Levenberg-Marquardt algorithm)		x
	Week 48	24.11 - 30.11
	document the results of the two-tensor tractography given a tensor volume		x
	Try to do mutli trace tractography given a DWI volume		x	Mon Nov, 17th
	Week 47	17.11 - 23.11
	Working on Python tractography module for multi fiber tracing given a tensor volume		x	Mon Nov, 17th
	Week 46	10.11 - 16.11
	Get vertex data out of the nvert nrrd filled by the tractography back to Slicer		x
	Try to pass image data from Python to Teem through nrrdWrap_nva function		x
	Try to generate a list of point locations that were used as tractography seedpoints in the VTK tractography		x	Thu Nov, 13th
	Implement Python tractography module for single fiber tracing given a seeding starting point and a tensor volume		x	Fri, Nov, 7th
	Week 45	03.11 - 09.11
	Try to get image data from numpy (= Python package) to Teem nrrd struct		x
November	Week 44	27.10 - 02.11
	Try to get image data from numpy (= Python package) to Teem nrrd struct		x
	Week 43	20.10 - 26.10
	Try to access DWI volumes through Python		x	Fri Oct, 17th
	Get Teem wrapped in Python		x	Fri Oct, 19th
	Week 42	13.10 - 19.10
	Try to implement the seeding part of the (VTK) one-tensor tractography module in Python		x	Tue Oct, 14th
	Week 41	06.10 - 12.10
	Try to implement the seeding part of the (VTK) one-tensor tractography module in Python		x	Tue Oct, 14th
October	Week 40	29.09 - 5.10
	Totally understand existing Python modules in Slicer		x
	understand existing one-tensor streamline tractography in Slicer (VTK)		x	Tue Sep, 23rd
	Totally understand existing Python modules in Slicer		x	Tue Sep, 23rd
	Week 39	22.09 - 28.09
	Slicer & Python Tutorials		x
	Enable Python in Slicer		x	Mon Sep, 22nd
September	Week 38	14.09 - 21.09

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