Alright, so we’re at a point now where:
- the FODs are not broken anymore (before with the huge ones in the CSF, that definitely was not the case); improvement is likely with SS3T-CSD, but what you’re doing now at least isn’t technically wrong anymore (again, it was kinda “wrong” before, with those FODs in the CSF)
- your seed sphere or region seems fine: you get streamlines alright, and somewhere in that “mess”, you can spot traces of structure though; so you’re definitely seeding in a WM tract at least
- ACT seems to then be the thing/addition that suddenly makes all streamlines disappear, unless I missed something
- So the 5TT image might be wrong / problematic / misaligned / …
But in the end, I think the key to getting results like in those last 2 photos, lies in defining 2 reasonable (separate) “end” regions of the tract. Not really “end” regions per se, but just 2 way points that are quite a bit separated along the tract. That requires streamlines to at least trace the part of the tract between those regions, and makes it very hard for them to deviate from that path (because they will otherwise likely miss one or the other region). For an example like this, I wouldn’t add the complexity of ACT, to be honest. If you choose your “end” regions well, there isn’t much reason to add more complexity: you should be able to get a decent tract between the regions. Once you got those, you should add each “end” regions as a separate -include region to tckgen. That then requires each streamline to visit both regions to be accepted.
Seeing that it’s @jdtournier in those photos there, I reckon he might be able to help you or inform you about the regions he used to generate that particular tract on display there.