#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://ljod.github.io/whitematteranalysis/
#Installation ###1. Install python. Anaconda is a nice option since it has VTK. ###2. Install the following python packages (dependencies).
- joblib (This can be done with easy_install, for example.)
- scipy (scipy is included in anaconda or EPD or other python distributions, possibly)
- vtk (vtk is included in anaconda or other python distributions, possibly)
####If your python does not already have VTK, compile it.
You will need to compile it with python wrapping. VTK_WRAP_PYTHON must be on. Make sure it finds the version of python that you want to use for this project, at configure time. 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 git and cmake. More information is at vtk.org. Then install it into your python: cd VTK-build/Wrapping/Python python setup.py install
###3. Install WhiteMatterAnalysis into your python.
cd WhiteMatterAnalysis
python setup.py install
###4. Test the installation. Run python, then:
>>> import whitematteranalysis as wma
This will produce errors if the required packages are not found.
###5. Please see the wiki for usage instructions. https://github.com/ljod/whitematteranalysis/wiki