Matthew,

Have you considered running a probabilistic or deterministic fibre tracking at all? I think

this might be more like what youre looking for. Conn is more suitable for fMRI functional connectivity,

whereas your analysis needs a ROI-based fibretracking. Great tools are the DTIstudio, FSL, SPMx and the

Freiburg DTI toolbox and MEDINRIA. All of these have robust fibretracking algorithms and are easy to set up.

cheers

niels