ENH: Update performance improvement for MI metric.
ENH: Run only one subject at at time

Nipype did not scale well to doing many subjects at once.
ENH: Download NiPype

Use a vacuous ExternalProject that does nothing but download the
Nipype source from github.  It would be possible to extract just
the git download script from ExternalProject_add, but it's more
complicated than just calling ExternalProject_Add.
Merge pull request #105 from BRAINSia/AddNipype

ENH: Download NiPype
ENH: Modified antsRegistration wrapper to allow multiple transforms.
ENH: Reworking filenames for readibility.
ENH: First attempt at adding ANTS template builder

The use of ANTS template builder for making a single subject
based atlas.
ENH: This version seems to work.
ENH: More progress towards a subject specific atlas generation.
ENH: Minor performance and style improvements.
ENH:  Needed to break processing down for debugging

The SGE_graph environment was causing massive problems
with the helium cluster submission.  I needed to break
it down into smaller units of processing.
ENH: Added data sink for initial subject template.
ENH: Added first attempt at PHASE_2 processing
Construction of framework
Mask editor for DTI

Index bug fix

Fix minor bug in the parameter number checking
BugFix: index bug fix in shuffling
ENH: Updated with changes that will require re-processing with NYPIPE.
ENH: Updated to use new ExtendedAtlas for BABC.
BUG: Fix Atlas processing

The atlas was hard-coded to assume that AIR was at index 0
and this was not always the case (i.e when the accumbens was
a specified region).
ENH: Use expanded grey matter regions

The tissue classifer can handle expanded
grey matter regions for segmentations.