Move all settings in pipeline to command-line arguments. Set conditional statements for all arguments to skip parts of the pipeline. Set labels as optional for tables.
Modify and expand the command-line arguments.
Fix override (return_missing) option in retrieve_data().
Update documentation to include installation of anaconda python environment (vtk can now build).
Raise IOErrors in ants.py functions.
Update pipeline and README, with new output and working directories.

Remove the save_xfm argument, because it seems the pipeline must save the transforms.
Update README to point to new LABELS file (copy of labels/protocol.py).
Add IOErrors to all functions that write out files.