incorporate SCIRun stimulated regions to connectome pipeline

[jessdtate]

make it so Simulations can easily be added to the connectomics

[jessdtate]

loop through monopolar runs, otherwise single runs

[jessdtate]

connectomeMover.py is a basis for this idea, but it needs redo

[mphook]

Collect all SCIRun-related outputs into a SCIRun_files folder. This would include the pial surface files from Freesurfer and the pts/edge/tangents/ends files for the whole brain tractogram from MRtrix. Those can be done automatically but other files such as the electrode transforms, and FEM brain outline would have to be done manually (for the moment).

The brainmask would probably be easy to automate using Freesurfer outputs and some thresholding either through nibabel or something else but the transforms need to be created through manual localization of the electrodes in a different SCIRun network. I doubt we want to dive into something as annoying as automated electrode location in SCIRun, so I suggest that stay manual for now.