ENH: Implementation of MSMT-CSD for estimation of fiber orientation distribution

[sebastientourbier]

Following #18 to integrate MRtrix3 MSMT-CSD for estimation of fiber orientation distribution

Tasks I see so far:

• Implementation of a new Nipype interface specific to MRtrix3 MSMT-CSD OR modification of Nipype interface for CSD already provided in CMP3 in cmtklib/interfaces/mrtrix3.py.

Note: MSMT-CSD would require to estimate response functions specific to each tissue class using dwi2response dhollander dwi.mif wm_response.txt gm_response.txt csf_response.txt [ options ] (see mrtrix3 doc page )

• Update of the main diffusion subworkflow and its subworkflow dedicated to the estimation of the fiber orientation distributions (in cmp/stages/diffusion/reconstruction.py). The local_model_editor and the local_model attributes of the class MRtrix_recon_config should be revisited to allow selection of Tensor, CSD, and MSMT-CSD. Workflow should be updated or inputs/outputs of interfaces should be rearranged appropriately with the new OR modified interface in the function create_mrtrix_recon_flow.

Note: Other new class attributes/traits (parameters) can be added in MRtrix_recon_config if needed.

• If necessary, rearrangement/Reconnection OR update of the main diffusion workflow (in cmp/pipelines/diffusion/diffusion.py), this might involve updating outputs to be sinked to the main CMP3 outputs (<derivatives>/cmp/dwi).

• If needed, new attributes/traits can then be easily integrated and tuned in the graphical user interface by an appropriate update of the corresponding graphical component, implemented in cmp/bidsappmanager/stages/diffusion/reconstruction.py