Hi Roey,
Sorry about the radio silence – we’ve all been a bit overwhelmed with ISMRM and preparations for the MRtrix workshop last week.
As you’ve already figured out, the difference will be related to the change in default for tckgen -cutoff option, along with a minor contribution from a bug fix in our handling of the spherical harmonics (this is unlikely to be related to the issue you linked to though). We tried to alert users to this change, since it was definitely going to introduce differences… Choosing an appropriate default threshold is not as trivial as it sounds, as you’ll see from the lengthy discussion we had over this on GitHub. It boils down to the inherent differences between the old CSD and the newer MSMT-CSD version, in particular with regards to how the non-negativity constraint is implemented (soft vs. hard respectively). Since tckgen doesn’t inherently have knowledge of how your FOD image was generated, a one-size-fits-all default cutoff isn’t always appropriate. However, since our recommendations are now veering heavily towards the use of multi-tissue CSD (even for single-shell data), we have decided to use adopt a default threshold more appropriate for that algorithm…
I hope this clarifies a few things…?
All the best,
Donald.