Generalize .sh scripts

[ebald19]

The shell scripts for the original DYNACT workflow are progressive repeats with subject names replaced. These scripts should be refactored so that:

1. There are no hard-coded file paths to home user directories.
2. There are no repeated code-blocks
3. They take arguments to be re-used in the future if necessary.

Please create a new branch off the develop_clean branch to make these changes and create a PR to merge them back in.