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Dear FSL experts, I have run probtrackx2 with a seed mask (left SPC) and a target mask (left DLPFC) but I'm in doubt about the correctness of my results. I'm interested in the proportion of streamlines from the seed that reached the target, as well as in extracting the tract-specific FA values. I used the same mask simultaneously as a target, waypoint and a stop mask. To my understanding, the waypoint mask should restrict the streamlines to only those passing through the mask (in my case the target mask), shouldn't it? However, when I view fdt_paths.nii in fslview, this doesn't seem to be the case (there are some streamlines that leave the seed but don't seem to pass through the waypoint mask). I'd be happy to send you a screenshot from fslview and the output from FDT, if needed. I'm using FSL Version 5.0.4. and the following command line: probtrackx2 -x leftSPC.nii -l --onewaycondition --omatrix2 --target2=leftDLPFC.nii -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=struct2diff.mat --stop=leftDLPFC.nii --forcedir --opd -s merged -m nodif_brain_mask --dir=seed2target --waypoints=waypoints.txt --waycond=AND --targetmasks=targets.txt --os2t Any help is greatly appreciated! Best regards, Lora