ENH: Modified atlas xml name
ENH: Added print statement to diagnose missing sentinal file
COMP: Remove global declarations from GenericTransformImage.h
BUG: Uniformly apply modify_qsub_args for configuring qsub_args.

There was a wide array of options for the modify_qsub_args that were
not uniformly applied or implemented.  By using modify_qsub_args
consistently and uniformly we can simplify testing and reduce
problems with running these experiments.
ENH: Allow template building to only do new files

It is desirable to simply skip sessions that are
completed so that the cluster is not bombarded with
unnecessary qsub jobs.
ENH: Add code for identifying the brain stem

This is an initial step toward robustly identifying the brain
stem from a set of images.
BUG: ATLAS_DIRECTORY to ATLAS_INSTALLING_DIRECTORY