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Hi Kristen, When you choose this option in probtrackx, there is no threshold to choose. it just makes sample streamlines more likely to stop in regions where the volume fraction of the anisotropic compartment is low (i.e. low anisotropy). It makes your tractography more specific but less sensitive, and it would probably mean that you will need to increase the number of samples to get sensible estimates of the path distribution. I don't have much experience using this option, but I think it is better to avoid it. I would favour using waypoint/exclusion masks, and let the estimate of the uncertainty on the PDD do its job, which is that tracts will spread when you are uncertain about the PDD. Cheers, Saad. On 25 Mar 2009, at 18:15, Lindgren, Kristen, Ann wrote: > Has anyone used the option in probtrackx to constrain tracking using > anisotropy? If so, how did you go about choosing your threshold > level? Any advice or references would be helpful. Thanks! > > Kristen Saad Jbabdi Oxford University FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222545 (fax 717) www.fmrib.ox.ac.uk/~saad