ENH: Fix logic bug for testing program.
ENH: Fixed FS Logic for running Freesurfer Template building.

The scripts to run freesurfer template building were not properly formatted.
BUG: Fixing errors in freesurfer running.
Denosing inputs of BRAINSCut

Minor delete of comments
BUG: Still tracking down freesurfer failure cases.
Merge pull request #173 from reginakim/DenoisedInputForBCut

Denosing inputs of BRAINSCut
ENH: global value is configurable from the command line and the configuration file.

Usage:
    baw_exp.py --ignore_datasinks ...
       Sets GLOBAL_DATA_SINK_REWRITE == False

    In configuration file:
       [PIPELINE]
       IGNORE_DATASINKS = True

       Sets GLOBAL_DATA_SINK_REWRITE == False