Hi If you want streamlines from A to B and not beyond, you should use these options: probtrackx2 --seed=A --waypoint=B --stop=B --onewaycondition Cheers, Saad On 7 Jan 2016, at 13:18, Seung-Goo KIM <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts, May I ask a question about probtrackx2? Maybe I still don’t understand how ‘way-point mask’, ’target mask’ ‘stopping mask’. I want to get tracks only between two masks (A & B). So I set two regions as seeds and ran network mode: probtrackx2 --network --forcedir -V 1 -s merged -m nodif_brain_mask.nii.gz -x seedlist.txt -o vmap --opd --pd -P 10000 --rseed=57967 Although I could get a connectivity matrix but the visitation map includes all tracks started from A (blue) and passing B (green) and go further beyond B, which is different from what I want: <Screenshot - 01052016 - 12:54:46 PM.png> Although it may not make much sense with these close ROIs… But the idea is to get tracks that only connects two regions. What should I do for that? Thank you in advance. Best, -- Seung-Goo KIM ------------------------------------------------------------------ Saad Jbabdi, PhD Associate Professor MRC Career Development Fellow FMRIB Centre, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK. tel (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>