hi Luca –
We are in the process of putting out a new release this week and will be updating our website to match. We’ll be updating the sections on tractography.
The option for multi-threading means that BrainSuite will run parallel jobs for finding the tracks. If you have a CPU with multiple cores, then this will speed up the computation. For example, if you have a quad-core hyperthreaded CPU, then BrainSuite will launch 8 threads for the computation, and it will be about 8 times as fast. One side effect of the parallel computation is that the order in which the tracks are found is non-deterministic. This is why we have the sort option — it reorders the tracks to be consistent with the single-threaded version. The track order probably has no effect on most applications, but it is useful if you want to compare processing, e.g., compare results from two different computers (we use this to test Mac vs. Linux vs. Windows).
Many of the other parameters may be dependent on your own data. The angle threshold controls how much the tracks can bend at each step, so how you set this may depend on the anatomy you are studying. Increasing it may produce extraneous tracks. The FA threshold is useful for constraining the tracking to the white matter when computing tracks in DTI; similarly, the the GFA/L2 threshold can be used when using the ODFs. You can use the mask tool to explore the effect of different thresholds on the boundaries in your image. For the FA threshold, you might try a range between 0.1 and 0.3.