Waypoints and Stop Options using Probtrackx command in FSL

Good morning,

I am Daniela Lizarazo, currently using FSL to perform tractographies for images of white matter tracts associated with the pre(SMA) in people with huntington’s disease and controls.

I was surprised to see that when I performed the probtrackx command with the stop option at the ROI (We choose the caudate for this time), the results of the image were much bigger than the images resulting from a probtrackx with the waypoints command. In the first case, we got a tractography representing what seems to be all of the white matter tracts of the hemisphere defined while the waypoints option gave us a better approach of the tract we were looking for (Frontal Striatal Tract).

If I understand correctly, the opposite should happen: Waypoints gives a bigger image than stop.

Any idea why this might happen? Help!?

Thank you in advance and kind regards,