Dear MRtrix3 experts,
hello, I am a new user of mrtrix, and even new to all the command line stuff.
I successfully installed all mrtrix3 tools, but I do not know how to access to the data in my local computer.
Maybe I should work on the Compiling external projects with msys2?
or is there any other suggestion or am I missing out something ?
I am completely lost… help me out.
Thank you.
To get started on the command-line stuff, I recommend you have a read through our brief Introduction to the Unix command-line.
You mention set_path in the title of your post, but this bears no relationship to accessing you data – it only ensures that the commands you’ve just installed are available on the command-line.
I’m not sure what this is about… But once you have MRtrix3 installed (I’m assuming you made it that far?), then there should be no need to compile anything else – all the compilation required should already have been done.
By default, your home folder when you start an MSYS2 terminal is located within the home folder, itself contained within the folder where you installed MSYS2. You should be able to navigate to your own Windows home folder with:
$ cd /c/Users/yourusername/
obviously, you’ll need to replace yourusername with your actual username in the above command. From there, you’ll be able to see your own Documents, Desktop, etc. (using e.g. ls).
Note that you can set your MSYS2 home folder to be the same as your Windows one with this simple trick (this is how my laptop is set up).
Once you have found your way around the command line, I’d recommend you have a look at Marlene Tahedl’s B.A.T.M.A.N tutorial https://osf.io/9wjy4/ and our beginner section in the docs https://mrtrix.readthedocs.io/en/latest/getting_started/beginner_dwi_tutorial.html.