I’m not sure I understand what you mean here. Which aspect of the FSL tractography pipeline are you trying to replicate? I suspect one of the various seeding options will be suitable for what you’re after (maybe -seed_grid_per_voxel?), but hard to know from your statement…
No, this is a parameter used for the rejection sampling that is used to obtain a fresh random sample from the fibre ODF at each step of the streamline. Briefly, at each step, the streamlines algorithm needs to determine the direction of the next step. With deterministic tracking, that’s just the nearest peak in the fODF (of the major eigenvector if using tensor tracking). With probabilistic approaches, we need to draw a random direction from the fODF - in tckgen, we use rejection sampling for this. It works by drawing a sample direction from the uniform distribution, then accepting this direction with probability proportional to the amplitude of the fODF. Obviously that means many samples will be rejected before we find one that is accepted. The -trials option sets how many attempts to do at each step in the streamline before giving up. The idea being that if the fODF is sub-threshold over the entire acceptable range of directions, then no samples will ever be accepted, so we need to give up at some point and say that the fODF is too small to track at this point, and hence we terminate the streamline.
Because if the probability of a path segment is the product of the probabilities for the path tangent at each sample point, then this path segment probability becomes dependent on the number of sample points. But if we take the product of sample point probabilities and raise it to the power 1/ nsamples, then that should counter that effect (in practice, it’s a little messier than that, we’re still discussing the best way to deal with this internally - but I won’t go into it here).
Ah, OK, I think this answer my first point.
No, this controls how hard to try finding a suitable starting direction from a given seed point. The idea being that the initial direction of tracking should also be selected at random, but most directions will not be eligible due to being sub-threshold. This is the same issue as the -trials issue above. If there are no suitable supra-threshold directions in the fODF for that seed point, we need to stop trying to find such a direction at some point. This is what this option does. But once a suitable direction is selected, the algorithm will not re-visit that seed point.
I think what you’re after is probably the -seed_random_per_voxel or -seed_grid_per_voxel options. These will guarantee the same number of (attempted) seed points for each voxel, although the locations of these seed points will be distributed throughout the voxel, rather than limited to the centre of the voxel.