Updating these files to integrate atropos into pipeline (WIP).
Belated commit representing the first round of modifications to the pipeline in regards to adding Atropos and Atropos correlation to the pipeline.  Atropos modules are currently added as the final step; they will need to be moved to before the statistics step.
Merge branch 'master' of https://github.com/jamesjcook/seg_pipe_mc
Updating code per James' advice before altering command_line_mc issue.
Updated so that only one runno needs to be entered for DTI channels, eliminating tediousness and unneccessary opportunities for error.
Have also switched the order of the runnos and the source/destination folders.  For the sake of simplicity, will switch back in next commit.
Returned the commandline to its original format of requiring the command to end in "runno1 runno2 ... source_project destination_project". \n
Had previously switched it to "source_project destination_project runno1 runno2 ...".
In conjunction with command_line_mc update 17 Sept 2014.