BUG: Missed brainmask read read wrapping

Allow XML files to have relative paths to images, this includes
the head mask and brain mask.
ENH: Refactoring template.py for consistent data sinks.

Fixing Template generation from data sinks
ENH: More changes to get atlas generation cleaned up.
BUG: Incorrect file was used for selecting the brain mask.

The brainmask label was incorrectly using the BRAINSCut outputs.
BRAINSCut is not always available, and it is the wrong mask to be used
for clipping the head postieriors.
STYLE: Remove unnecessary code.

There were unnecessary data sinks that seemed to have no purpose.  Those were removed.

There were conditional statements for options that seemed to have no current purpose. Those were removed.
BUG: Data grabber changes required dictionary changes

The changes to the data grabber required changes to the images dictionary.
The images dictionary needs to be order for inputing into the ants average generation.
BUG: The master atlas should be specified from config file

There was an incorrect assertion that required coupling of the template to the
previous experiements CACHE directory. This was incorrect.  We explicitly want
each stage to be separage and only dependant on the RESULTS directories.

It is anticipated that the CACHE directories will be deleted soon after
the experiements are run.
STYLE: Remove global code from __init__.py

It is bad to have globals, and to rely on them being loaded with pythons
default module loading capabilities is even more confusing.  Simplyfy by puting
the variables in the smallest possible unit where they are need so that they are
scoped only to the code location where they are needed.

This patch also adds a feature to the MakeAtlasNode so that only subsets of the data grabber
are used.  This allows for smaller more granular data grabber nodes to be created.
BUG: Command line wfrun argument was not being respected

The pipelines were hardcoded to run as SGEGraph.

Localizing related features in one file so that exposure can be minimized.

The behavior for configuring the pipeline name and arguments was convoluted and spread
across several files.  It was difficult to determine where items were being set.
STYLE: Remove unnecessary checking

It is not required, or desirable that the current plugin archetecture is the same
as the default.
BUG: The logitudinal processing could not occur previously

The logitidinal step of processing based on this subjects reference atlas broken.
There were confounds between the stages that needed to be separated.
ENH: Add separate config variables specific to each workphase

It is desirable to have only one configuration file for an entire
data processing stream.  This breaks the variables apart for each
phase so that we can have a single configuration file that is
capable of being used for all phases.
BUG: Premature return from loop

There was an in-advertent return from a loop such that only the first
session was being processed.