Fixed some uses of niftiSetQto and niftiCheckQto to both use niftiSet calls.
Finalizing of multiple TODOs which required clean-up that were left over for post-Inplane load process implementation.
Fixing a few bugs based on the latest changes.
Responding to comments from pull request 24. Cleaned up a comment and a warning.
Further changes to warning.
Merge pull request #24 from vistalab/setQtofix

Cleanup of code post-Inplane Functionality Merge.