I am interested to implement the various tractography algorithms of dMRI data. I wanted to use this software in Windows OS. I followed the instructions and has installed MSYS2. But I am not able to find the command to open the MRtrix 3 and start inputting the commands. Could anyone provide me some clue to get started and also when I went through some tutorials I am not able to understand how to give the file as an input. I have files of dMRI data downloaded from ISMRM 2015 and I have stored the files in my local PC.
Also, is it a better option to run the tractography algorithms in Windows OS through MSYS.