Problem with Mrtrix3 installation

Dear all,
I’m trying to install mrtrix3 via MSYS2 on windows.
I have follwed all the instructions, but I found a problem on configuring mrtrix.

You will find attached all the installation process with the configure.log file.

Your help is well appreciated.
thank you very much.

Dear @TR-Abir

I didn’t look at the exact problem you have, but something you can try is running MRtrix using containers (Running MRtrix3 using containers — MRtrix 3.0 documentation). If you don’t know much about containers, you’re welcome to check the brilliant introductory video on this page:

The issue is more complicated however if you wish to run GUI (as Windows does not support X11 graphics natively). One solution I can recommend is Neurodesktop. It is a lightweight and easy installable Linux virtual machine that includes X11 graphics and was built especially for neuroscience data analysis. It comes with MRtrix3 built it, so you don’t need to install anything on top of it. To install Neurodesktop, just go here and press on Windows.

When you have neurodesktop running, you can find MRtrix in the start menu under Neurodesk → Diffusion Imaging → mrtrix3 (check here for which MRtrix versions are available: Applications | NeuroDesk)

I’m contributing to both neurodesktop and MRtrix3, so you’re welcome to post here any questions you might have on using MRtrix3 within neurodesktop.



Given that you’ve installed the mingw-w64-x86_64-gcc package, the g++ command should be available. But the error you’re getting is that it can’t find g++. The main reason I can think of for that to happen is that you might not be running the mingw64 shell. On my system, if I start the mingw32 or msys2 versions of MSYS2, I get exactly the same problem as what you’re showing. You can check which version you’re running if you type


which should return /mingw64 if you’re running within the correct terminal.

If that’s not the issue, then please provide the output of:

$ echo $PATH

Maybe you’ve made some modifications there that would impact on where the system looks for its executables…

All the best,

Dear @orencivier Thank you for the information.

Dear @jdtournier your help is well appreciated, it’s right I’m not running the mingw64.
the problem was fixed when I have runned mingw64.
Thank you very much.

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