yohanyee / minclaplace

Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries

minclaplace

All the glories of Laplace's equation for measuring cortical thickness as initially described in:

Jones SE, Buchbinder BR, Aharon I. Three-dimensional mapping of cortical thickness using Laplace's equation. Hum Brain Mapp. 2000 Sep;11(1):12-32.

and modified somewhat in:

Lerch JP, Carroll JB, Dorr A, Spring S, Evans AC, Hayden MR, Sled JG, Henkelman RM. Cortical thickness measured from MRI in the YAC128 mouse model of Huntington's disease. Neuroimage. 2008 Jun;41(2):243-51.

Can be used anywhere two boundaries can be defined and the path from one boundary to the other has some intrinsic meaning. The cerebral cortex is the classic example, though it has been applied to bone cortex, plaque thickness, etc., as well.

Usage

Detailed usage examples to come

Installing

python setup.py install

(If you want to specify the install location, add the --prefix option, i.e.: python setup.py install --prefix=/some/directory)

Requires numpy, scipy, and pyminc (version 0.3 or greater).

Compiling

The setup.py script uses the cython generated C code; to regenerate that C code, i.e. after making changes to cython_laplace.pyx, run:

python setup-cython.py build_ext --inplace

Note that you need cython version 0.16 or greater.