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 reference 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. InInternational Conference on Medical Image Computing and Computer-Assisted Intervention 2012 Oct 1 (pp. 123-130). Springer Berlin Heidelberg.
For projects using Slicer please 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."
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
Note: If you decide to use another python that does not already have VTK, you can compile VTK.
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
7. Please see the wiki for usage instructions.