pythonize the pipeline

[jessdtate]

convert all the bash scripts to python to make it easier to script, package, maintain, and expand. Slurm scripts would still be needed (or at least examples).

bash scripts to convert:

• calculate_connectome.sh
• Whole_brain_tract.sh
• HCP_to_subject.sh
• fs_heatmap

[jessdtate]

an alternate solution would be to generalize the wrapper for the command line calls. Which is similar to what the python API does.