Updated defaults to those suggested by @rybern

Also reorganized ordering of some options
Fix indentation
Add study 550 to batch processing
Added more useful filtering functionality

Filtering will now accomodate our immediate use-cases for fresco (can still definitely be expanded upon though). Fixed bug in filtering that was already present before my modifications.

Fixes #24 #25 #26.
Merge pull request #27 from jrrideout/real-data-prep

Filtering, bug fixes, and a few misc. changes