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Hi Leslie, there is not an automated method for thresholding path connection probabilities. The issue has been discussed a lot in the list, you can find lots of information there. In short, try to use as much prior anatomical knowledge to restrict the pathway propagation using waypoint, exclusion, termination masks. Also, you can choose a reasonable % threshold (using the waytotal value), again driven by what you would consider plausible, given the anatomy. Cheers, Stam On 30 Sep 2011, at 10:06, Leslie Engineering wrote: > For probabilistic tractography, how does one choose an appropriate threshold. I would imagine it is dependent on the number of voxels in the seed ROI and the number of samples (default 5000). > > Is there an excepted method? > > Thanks!