Fixes and cleanup

I run all functional metrics on a dataset, cleaned up and rearranged the code, fixed some problems with the documentation.

Two most noticeable changes involve Frame dispalcement calculation. I changed the radius to 50 (from 80) which is consistent with FSL scripts, Power paper and documentation. I also fixed the total number of frame displacemnts which should be len(timeseries)-1 not  len(timeseries)-1. It would be great if someone could review these changes.