Hi @blezek,
The SS3T-CSD would be in dwi2fod if it were available… but it’s not available yet indeed. The above linked abstract itself however, is on the unsupervised response function selection algorithm that is available in dwi2response, more specifically as the “dhollander” algorithm choice in that command/script. This algorithm’s goal is specifically to obtain the WM, GM and CSF responses directly from the DWI data. It works for both multi-shell as well as single-shell (+b=0) data. In case of “true” multi-shell data (3 distinct b-values, including b=0), the responses are then suitable for MSMT-CSD (dwi2fod msmt_csd). For single-shell (+b=0) data, you’d have to input them into SS3T-CSD (once I make it available at some point in the hopefully-not-too-distant future). Alternatively for such data, you can ditch the GM response and do an MSMT-CSD with only 2 tissue types (WM and CSF) (happily read the rest of that thread to get as much context as needed). You don’t get to enjoy the benefits of a GM response then of course. Here’s some further information on dwi2response and dwi2fod algorithms, and some relations and potential combinations.
In the context of the original question of this thread though: @Carlos_Gutierrez seems to have multi-shell data, which would work well the global tractography algorithm available in tckglobal. This is a multi-shell multi-tissue global tractography algorithm, that works directly on the DWI data (no explicit CSD step of any sorts, but the same “model” and assumptions with respect to the DWI signal are inherently used and relied upon in the method). With multi-shell data (3 distinct b-values, including b=0), that method could generate a track(segment) distribution that represents the WM, in addition to GM and CSF isotropic signal compartments. In the absence of multi-shell data, it can (similar to MSMT-CSD theory here) also just go for the WM track distribution together with only a CSF compartment. Again, you wouldn’t benefit of all that a GM response can bring additionally in ensuring a good as well as meaningful fit.
But so, in @Carlos_Gutierrez’s case, he can benefit of the dwi2response dhollander algorithm to get his multi-shell WM, GM and CSF responses, which can then feed into tckglobal.
I hope this all makes sense. Don’t hesitate to ask for clarifications if it doesn’t. 
Cheers,
Thijs