STYLE: Updated README to include Python-specific information on building
Update README

Fixed CMAKE cache variables to set:

http://www.cmake.org/cmake/help/v2.8.10/cmake.html#module:FindPythonLibs
ENH: Start of a DWI Processing Pipeline

This pipeline uses both FreeSurfer and BRAINS
and DTIProcess to get regional measures from
DWI data.
ENH: Remove pycharm working directory.
Merge pull request #29 from dmwelch/master

STYLE: Updated README to include Python-specific information on building
ENH: Creating DWI processing stream.
ENH: Changed pathing for generating python nipype wrappings.
ENH: Added features to allow for upsampling

An optional feature is adde to specifying the output image
sampling via a referenceVolume specification. Also, since
it is often needed to have reference B0 image one can also
specify extracting the first sub-volume as a separate image.
ENH: Updated SEMTools definitions with new build

Ran autopep8 to make code compliant with NIPYPE standards.
ENH: NIPYPE updated antsRegistration interface.

Units must now be specified for the shrink factors.
ENH: Added prototype for DWI processing.

This is still a work in progress, but it's a good start
towards doing DWI processing in ACPC space.
COMP: Resolved compiler warning.
STYLE: Remove references to BRAINSStandAlone and replace with BRAINSTools.
BUG: Fixed final transform, updated the resampled output volume and other outputs accordingly
ENH: fixed all failing tests except acLowerBound, added translation of AC to origin as final step if atlas-registration mode is used.
STYLE: Code review of Ipek BCD changes

Removed dead code comments,  Removed debugging file writing,
Re-organized code to be more compact failure logic, fixed ITK style issues
Identified several places that need further investigation.
BUG: Removed aliased variables that were used inconsistently.
STYLE: Conform to ITK style.
ENH: When copying transforms, both FixedParameters and Parameters must be set.
ENH: Step 1 in decoupling outputs from transform estimation.