zeigar/whitematteranalysis

White matter tractography clustering and more...

whitematteranalysis

Synopsis

White Matter Analysis provides clustering and tractography analysis tools.

It implements algorithms from publications listed here: http://projects.iq.harvard.edu/whitematteranalysis/publications

Also see the github.io page here: http://slicerdmri.github.io/whitematteranalysis/

Please cite the following papers:

O'Donnell, LJ., and Westin, CF. Automatic tractography segmentation
using a high-dimensional white matter atlas. Medical Imaging,
IEEE Transactions on 26.11 (2007): 1562-1575.

O’Donnell LJ, Wells III WM, Golby AJ, Westin CF. Unbiased groupwise registration of white matter tractography.
In International Conference on Medical Image Computing and Computer-Assisted Intervention 2012 Oct 1 (pp. 123-130).
Springer Berlin Heidelberg.

For projects using Slicer please also include this text (or similar):

"We performed tractography visualization with anatomical hierarchies in 3D Slicer (http://www.slicer.org)
via the SlicerDMRI project (https://github.com/SlicerDMRI), funded by NIH U01 CA199459."

Installation

1. Download whitematteranalysis from github.

  git clone https://github.com/SlicerDMRI/whitematteranalysis.git

2. Install python.

Anaconda is a nice option since it has VTK and scipy. First install anaconda from http://continuum.io/downloads, then run:

  conda install vtk

3. Install the following python packages (dependencies).

Once you have anaconda installed, run:

  pip install joblib

Other distributions, or self-compiled, Python will require installation of scipy.stats, scipy.optimize, and statsmodels, depending on the usage.

Note: If you decide to use another python that does not already have VTK, you can compile VTK.

• VTK: http://www.vtk.org/Wiki/VTK/Building
• http://www.vtk.org/Wiki/VTK/Git/Download

You will need to compile it with python wrapping. VTK_WRAP_PYTHON must be on. Make sure that at configure time it finds the version of python that you want to use for this project. You may need to toggle t for advanced mode in ccmake. I have something like this when I run: cd VTK-build ccmake ../VTK

   PYTHON_EXECUTABLE                /Users/lauren/anaconda/bin/python            
   PYTHON_EXTRA_LIBS                                                             
   PYTHON_INCLUDE_DIR               /Users/lauren/anaconda/pkgs/python-2.7.4-1/in
   PYTHON_LIBRARY                   /Users/lauren/anaconda/lib/libpython2.7.dylib
   PYTHON_UTIL_LIBRARY              /usr/lib/libutil.dylib   

Note this requires both git and cmake. More information is at vtk.org. To install your compiled vtk into your python: cd VTK-build/Wrapping/Python python setup.py install

4. Install WhiteMatterAnalysis into your python in the standard way.

 cd whitematteranalysis
 python setup.py install

5. Please see the wiki for usage instructions.

https://github.com/SlicerDMRI/whitematteranalysis/wiki