Dwi2fod msmt_csd - WM GM CSF Mask and tckglobal in patients

Hi MRTrix Team and Community,

is there a way to produce the Masks of WM GM and CSF as a byprodukt of the dwi2fod msmt_csd script?
As I understand correctly is the 5ttgen Algorithm only for the anatomy (MPRAGE,…). What does the " dwi2fod msmt_csd do, since you dont have to give the script an anatomie file. How is it calculating the different tissue types?
Second question would be the “tckglobal” algorithm? What is it doing exactly? You dont give it the FODs from the dwi2fod only the response functions. Is it calculating new FODs, and second is it doing some tissue type masking or something? I need to know, because diseased tissue of patients have a similar Grayvalue like the CSF. I just want to be sure, that I dont miss something, going throug the tissue. How can I be sure? Whats the best approach, that I dont miss something?



Hi Ralf,

I would suggest reading the journal articles for which the references are embedded in the help pages of those relevant commands.