Using dMRI for diffusion data


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.

Welcome Strivathsav!

It’s not 100% clear exactly the point at which you are stuck. You state that you have installed MSYS2, but have you additionally installed MRtrix3 as well, via the package download or building from source? MRtrix3 does not come bundled with MSYS2.

Once you have installed MRtrix3, it is not a matter of “opening MRtrix3 and running commands”: all MRtrix3 commands are available at the command-line that opens when you run an MSYS2 terminal. If you type in the name of an MRtrix3 command and the terminal states “command not found”, then either the MRtrix3 installation was not properly completed, or the files are present on your system but their location is not present within your PATH environment variable.

Hopefully once you can actually start running commands, the way in which image files are provided to commands will become clear based on following the tutorials; but it sounds like the first step is verifying that MRtrix3 is actually installed properly.