Fixed issue from last check-in: need to resample files after lsq12 registration prior to running mincANTS.
Related changes:
Created LSQ12ANTSNlin module that does lsq12 registration, resampling of files and mincANTS call.
Includes associated changes to: MAGeT_modules, registration_chain and pairwise_nlin

Other minor changes and bug fixes:
1. Moved createMask out of HierarchicalMinctracc. Changed argument to defaultDirectory. Default directory changed to tmp.
2. LSQ12 module. Changed function name from buildCommand to buildPipeline for naming consistency with other modules.
3. Registration_chain.py now uses full stats calc rather than removing lin_from_nlin.
4. setLastBasevol() with no argument now uses original input for each group instead of original input file. (This was problematic for MAGeT with new LSQ12ANTSnlin module.)
5. Fixed error in stats_tools hwere transform and inverseXfm not being set properly in statsGroup. Added setupXfms function to __init__