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Hi there, I'm trying to use probtrack2 to run tractography from a region in the brainstem up to the cortex using a seed mask and 3 waypoints (with exclusion across the midline). Using the default settings, I seem to be getting inclusion of cingulum and a lot of spurious wisps. I've been trying to figure out the optimal settings for this analysis but I was hoping you might be able to suggest some things to help. Is there an optimal curvature threshold for a path that essentially goes from motor cortex into the brainstem (almost a straight line)? I tried using the waypoints specified in their order but this didn't seem to help. I have also tried using -thrP in fslmaths to threshold, but this still doesn't seem to get rid of the small random wisps (and ends up cutting into the tract before those go). This is very high resolution data (1.25mm^3 voxel size) so I'm hoping to get a crisp result in the end. I really appreciate your help! Best regards, Meriel