(Sounds great! I would be very happy if we can put PTT into MRtrix3! More below…)
Thank you very much for the detailed answer.
Judging from the code, I was suspecting that this was the case. The link for your previous discussions on default values is very informative. Also @jdtournier’s paper is a great reference for iFOD1 - I will certainly use it.
About the power parameter - @jdtournier also suggested (during my ISMRM talk, the previous year) to modify power instead of step size or sample in order to modify streamline dispersion. Basically the “sharpness” of FOD lobes determines the dispersion and similar effect could be achieved outside the tracking algorithm by modifying the FOD image (maybe you already thought about this to further speed up iFOD2). Nevertheless, my point is I think the default power value should also depend on the SH order in addition to nsamples.
I read that this was mentioned by you before also, but it would indeed be great if there is a more comprehensive paper about iFOD2. Especially it is hard to follow the calibration part from the code.
For PTT (actually starting from its prefecessor in Aydogan et.al., MICCAI, 2016), we started coding everything from the beginning in order to have an algorithm development platform. So I implemented SH expansions, interpolations and etc. in MATLAB. Computing one streamline was taking tens of seconds I then had to gradually convert modules to mex codes which really sped things up. At that point, we had a fast and flexible platform and we decided to share our code. So I thought, “let me spend the next month or two to write everything in C/C++, I already have most of the stuff in mex anyways”, then after 2 years, Trekker was ready Well, we are extremely happy and proud that we could put it together at the end. We are now able to write real-time tractography applications with PTT. As you would also agree, without your own code, it would have been difficult to implement algorithms/applications. However, for implementation and sharing sake, it would have been much easier for us to use an existing platform like MRtrix, Dipy, etc. It is never too late though, I would be very happy if we can put PTT into MRtrix3!