Hi-
Did you try just running deterministic ("-mode DET") tracking first? As noted in the help/scripts, probabilistic tracking methods for HARDI data rely on very heuristic uncertainty measures at the moment.
Also, I am not sure what a recommended threshold value for GFA would be-- basically, voxels with GFA values above that threshold are considered in the WM, and therefore tracked, while those below it are excluded from tracking. In the DTI case of having just FA, for adult humans a threshold value of FA>0.2 is typically taken across the field as a good proxy for WM; in human infants, FA>0.1 is often used. For GFA, I am not sure if such a threshold applies-- that is worth investigating in papers that track that kind of HARDI reconstruction method. You can investigate what would be a good value in your data by adjusting the threshold and seeing what looks like a good WM map.
--pt