Add option to use the the ss3t_csd_beta1 algorithm for single-shelled data.

[ajschadler12]

• What is the current behaviour?
  • When provided single-shelled data, micapipe uses the "single tissue constrained spherical deconvolution" algorithm for FOD generation.
• What is the motivation / use case for changing the behaviour?
  • MRtri3Tissue is a fork of MRtrix3 (by Dhollander) which extends the multi-tissue FOD algorithm to single-shelled acquisitions.
  • FOD generation for WM, GM, and CSF is performed using 3Tissue/bin/ss3t_csd_beta1, on response functions generated using the dhollander algorithm.
  • The FODs can be used like normal in tckgen.

Since the program is still experimental, it may be best to turn on this functionality using a flag, e.g. -do_ss3t_csd (name taken from QSIprep).

[rcruces]

It's a great suggestion to extend the capabilities of our pipeline with this software. Again we encourage you to contribute with the development and implementation of new software and extended functionalities.