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Hi Catherine, You can use the --stop option (or termination masks in the GUI). If you merge both targets into a single mask (e.g. with fslmaths) that you use as a termination mask, then sample tracts that get to any of these targets will terminate there. Cheers, Saad. On 24 Feb 2009, at 12:26, Catherine Traynor wrote: > I am carrying out the connectivity-based seed classification using two > adjacent cortical target masks. I am concerned about paths that > appear to > travel through one of the target regions and on to the other. The > seed voxel > is then classified as connecting to both target regions for a single > path. > > What is the best way to deal with this situation? Is there any way to > terminate the path after it encounters the first target region, > without > having to run probtrack separately for each region? > > Many thanks > > Catherine Traynor > Saad Jbabdi Oxford University FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222545 (fax 717) www.fmrib.ox.ac.uk/~saad