Changes to MakeAverageDataset Pipeline for 2nd review

Supplemental/MakeAverageDataset/MakeAverageDataset.sh

Changes merged from pull request #36

1. Add -openmp flag to all calls to recon-all
2. Changes to work with volumes more efficiently
3. Readability improvements
4. Additional, optional arguments

Changes added after merge

1. Added support for positional specification of new arguments
2. Made sure main function does not use global variables set in the get_options function