Merge pull request #30 from binarybottle/hal-dev

Fix the last commit.  I'm not sure how to check it.
reverse a change in write_scalars() that causes problems
Merge branch 'master' of github.com:binarybottle/mindboggle
Move colormap.xml to the mindboggle_tools/bin directory
Update website users directory.
Fix close_surfaces() so that only label surface border vertices with the label are included.
Recenter and scale surface patches to fit within a unit sphere prior to running the zernike.py functions.  Test to make sure the outputs are consistent across the functions.
Remove option to close input surface for zernike.py functions. Move option to decimate input mesh to zernike_moments(). Reset defaults.
Fix bug in zernike_moments_per_label() where faces were overwritten.
Make changes to pipeline to accommodate changes to spectra and zernike functions.
Temporary changes to allow rapid debuging.
Hack to get around apparent Freesurfer bug where the Corpus Callosum
region of DKT40 annot labels are '3' instead of '0'.
Update data files to use Nick Tustison's OASIS (Atropos) template. Replace head templates with those built with antsMultivariateTemplateConstruction.sh.
Trying a lower iteration count to see if that helps deconfuse things.
Adding file to propagate fundus lines to tile the cortex.
Merge remote-tracking branch 'origin/ohinds-realignment' into ohinds-realignment

Conflicts:
	mindboggle/labels/boundary_realignment.py
replace Euclidean distance calcualation by vector subtraction and norm to speed up
Finding endpoints almost works, working on connecting via shortest paths.
Filled out implementation of shortest path, needs testing.
Keep using ANTS until figure out antsApplyTransforms...