act_anat_prepare_fsl: Improved initial brain masking

Script now uses FSL command standard_space_roi to perform an initial crude brain extraction prior to BET.
This now no longer relies on the input T1 image having a particular z-dimension with excessive neck coverage, and can also improve BET performance.
Documentation: added examples for simple workflows
Merge branch 'master' into C++11
Updated examples to reflect latest C++11 changes