It depends on what kind of connectivity value you are looking for. If you want to simply extract the number of tracts connecting two ROIs, you can do it in BrainSuite. There is a button under Menu–>File–>Save Connectivity Matrix can do it.
You want any further metric of the tracts (eg. Mean/Median of FA/MD), you need to use TractConnect tool (http://neuroimage.usc.edu/neuro/Resources/TractConnect)
Let me know if you have any further questions.