I am using MGH HCP Adult Diffusion data to explore connection between the cerebellum and cerebrum. The b-values are 1000 ,3000 ,5000 and 10000 s/mm2. However, I had noted that " Constrained Spherical Deconvolution … relies on single-shell high angular resolution diffusion imaging (HARDI) data, containing at least one non-zero b-value. Ideally, the b-value used should be in the region of 2,500 – 3,000 s/mm² (at least for in vivo human brains), although good results have sometimes been obtained using b = 1000 s/mm² data."
Can MRtrix3 be used in this case? Is there any parameter needed to be adjusted?
It can definitely be used! Higher b-values actually provide better angular contrast, which is what CSD relies on to separate different fiber orientations.
As the data you plan to use are multi-shell data, the best place to start is here: https://mrtrix.readthedocs.io/en/latest/constrained_spherical_deconvolution/multi_shell_multi_tissue_csd.html
Thanks a lot. By the way, when used for analysis of 7T dMRI from HCP, is there anything special needed to be adopted?